Due to the open nature of our driver system, it’s relatively straightforward to write a new driver file for almost any imaginable device in Nebula. However, driver development can be a pain, so I though I’d share some debugging tricks.
For all commands, we will navigate to the command line using windows Command prompt or powershell. Here I show command prompt syntax. Nebula is commonly installed under program files. So in the windows start bar type “cmd” and press enter. This should open the command prompt. The commands below navigate to the install location.
First, is the use of logging to the command line. When Nebula is launched from the command line, a series of optional switches can be used to report logged output. By opening this alongside the app, it’s very fast to figure out what or where something is going wrong. To see log output, use –printlog.
c:\Program Files\Nebula>Nebula.exe --printlog
This launches the app, but shows a live log output on the console at the same time.
Get a full list of Supported Drivers
This command will return a complete list of drivers found in the Nebula supported list. To print this list, use:
c:\Program Files\Nebula>Nebula.exe --listdrivers
Here is live example of that command and the expected result. A list of drivers is shown, press enter to close the listing.
Testing a specific Driver File
Next, let’s load up one of these drivers in the test utility. Now, this is where things get cool! The test utility can load a host device driver, inspect it’s shown devices, attempt to connect them, and even test every sub-device!
So, let’s assume we have a new camera driver we want to work on. The camera should do things like snap an image, show various properties etc. In my example I use a real UVC (web) camera, and inspect the driver. The driver actually pulls the real camera info and even snaps a test image. The goal of this function is twofold, first to validate a given driver, and second to validate the device itself.
For this command we will use –testdriver *drivername* and optionally –port *portname*, for example, COM5
Here we can watch the expected output in real time. Note a new window is spawned to show us the results for these tests.
Testing Host and Sub Devices
Let’s say we have a controller, for example, an ASI or Marzhauser box, which has a Z motor attached. In Nebula, the controller can be thought of as the Host (the resident controlling brain), and the device can be considered an appendage attached to the host. So all drivers must have a Host, but a Host may only have one device. In this example, we use a demo Focus device. First the host is loaded and analyzed, and then, you ca select to test any device provided by that host. I choose option # 1 (focus) and the test runs, even showing my driver has a small error I missed!
Obviously, if you have a driver which isn’t behaving, please contact us – yet I hope these options provide a first-line of interface for power users, so simple things can be corrected and analyzed quickly!
Thomas Spieker from Opto Gmbh was kind enough to send us a demo assembly of several microscopes made by his company. Opto manufactures a series of highly integrated microscope modules, all provided in a small, integrated form factor.
I was able to work with two different variations. One is a complete transmitted illumination setup with camera and objective at 20x. The second is a reflected light device with integrated LED illuminators.
It’s neat to see such a compact setup on the desk. Using the 20x with a typical gut section stained sample was a piece of cake. Field uniformity on the illuminator was great, and color balance was as expected.
The reflected design unit has both a coaxial and ring-style illuminator position – both are provided in Nebula as control LED options.
Use of the camera was straightforward. It supports 8 and 12 bit readout on a color sensor. I can definitely imagine hooking this up to a small XYZ gantry or even a 3d printer for inspection use. Thanks to Opto for the demo unit!
Here is a video review and live demo of hte unit while running on Starlyte Nebula.
Recently, I had two different requests to support the cameras manufactured by Touptek. Ash from Scientific Imaging was kind enough to let me borrow one for in-house integration and testing.
These cameras support Sony IMX-174 sensors, use a USB 3.1 (locking!) cable, and are straightforward to hook up and use. A GPIO connection is provided for I/O, and some models also have opto-isolated IO as well.
Binning, ROI and bit depth readout modes are also supported.
The camera I had hands on had a color version of the sensor, and while today has been a lot of rain, I was able to get a gloomy scene outside for my demo video below.
For questions on running this camera in Nebula, please contact us at www.starlyteimaging.com
If you are interested in these cameras, please contact Scientific Imaging.
Here is a brief video demo of the camera in Starlyte Nebula!
We had a recent customer asking to solve a rather standard but annoying problem. If I have a manual filter turret, and still want to overlay images, how easy is it to do?
To solve this, we added the ability to drag+drop any image from our capture sidebar into our main view. By adding a demo filter turret to the system config, we captured the real ex, di and em filter settings from the image, insuring metadata is transferred with the images collected. The resulting view is a true multi-dim architecture, saved as an OME set or RGB combined view. Our team made the addition, ran bug testing and edge case validation, pushed the changes and compiled the application in 1 business day.
Being able to react to our customers’ needs in a short timeframe is one of the best parts of working with my team. Nice work!
Over the past few weeks, we’ve been building out driver support for the Excelitas illuminator line. Today i wrapped the Tetrem unit up.
Below is a 2 channel illumination sequence using the Excelitas Tetrem, captured via a Hamamatsu Fusion camera. A nice feature of the Excelitas units is a commonality of protocol. By keeping the communication back end similar between different units, it’s a straightforward job to add new models as they release. Thanks to Gary Tokman from Visual Dynamix for allowing us the system access to get this done!
Each driver has a unique entry in the driver list. All drivers support the maximum possible device response time and full intensity range profile per device. The Mini will be added soon as well.
Contact us for more info at www.starlyteimaging.com !
Recently Tucsen had a presentation on their new Libra CMOS cameras which includes some nice improvements in sensor performance.
Key highlights were:
Improved QE at 92%
Large Full Well Capacity (48,000 e)
Native binning / debin system
In a recent presentation here a series of improvements were listed, among them a smaller pixel size selection option which supports a drop in pixel size to ~ 3.27um. From the explanation I assume the camera runs natively in a binned mode to produce 7.x um pixels, but can be optionally de-binned.
Each of the cameras (3 models announced) appear to have this feature, as shown below.
I’m more interested in the full well, as having a ~50k e full well seems a nice improvement in dynamic range over current options. Once item that was very interesting to me is that the full well capacity does NOT reduce when enabling the higher resolution mode. If this is correct, a 3.x um pixel with a 48ke full well would still be quite a nice bump in range and quite a feat!
For pricing, the presentation noted 0.4x the cost of a “classic CMOS”. I’m curious what that means in an actual dollar amount.
I made a short video describing why laser pricing is so different. Much of it comes down to how precise the beam performance needs to be, and as with so many similar fields, as precision becomes better and better, pricing begins to log scale up as the challenges increase. Thanks for watching!
ARC now has a driver available for users of Quorum Volocity microscopy software. New releases of Volocity will include native support. If you need a driver file or assistance please contact ARC for support.
One of the toughest aspects of working as a consultant engineer is that the coolest and most interesting projects are the ones I don’t get to talk about or share online! But as time marches on, sometimes I get to share a few of my secrets. One of those secrets is Zaber. Years back, I needed to find a reasonable cost linear motion system, with integrated motor drive, that provided a well documented library and good customer support. I ended up working with Zaber on that system, and came to rely more and more on their linear and rotary motion products for such systems. As I grew more familiar with these devices, Zaber released a few products into the microscopy industry, starting with an XY stage platform a few years back. Recently, Zaber released an entire microscope system. This microscope provides 3 channel LED excitation for fluorescence, a linear motor Z drive, motorized fluorescent filter cube changer, and XY top plate motorized stage.
One of the product engineers was kind enough to ask if I would give this new microscope an eyeball, so I spent some time with one of the younger employees at ARC to see if we could set it on fire or otherwise break it. 🙂 I’m happy to report it survived our abuse, no small feat for a microscope in my shop!
Unboxing & Assembly
Microscopes typically require a knowledgeable sales rep or service expert to build. As a test of difficulty and complexity for system setup, I decided to assign my relatively new employee Garrett to the build. His report from the build experience was insightful:
Overall, the assembly and the initial testing of the microscope was simple and concise. The assembly is pretty easy for a person’s first time building a microscope. The directions were clear and provided great examples of what to look for in terms of parts and what to do. The assembly itself wasn’t too hard as screws were accessible and easy to get to. It was also a little fun seeing the microscope work at the end of the assembly. The whole microscope was packaged in a pelican shipping case, so the parts were well protected. Directions were very concise and provided much detail aligned with picture guidance. The motor locks are very good, they never moved or slid in the slightest during assembly. Cable management is fairly good, doesn’t get in the way of any moving parts at any time. -Garrett Bunch
We also noted some areas for improvement along the way. For our model, the directions for mounting the microscope body and brackets, (5th hole) do not allow enough room for both the motor controller and the LED controller side-by-side as the picture shows. It would need to state at least the 6th or 7th hole. While used in all zaber systems, the the type of male cable connector for the X-DC02 cables were a little tricky to get connected. We had to fiddle with the inside thread on some of the internal drive connectors for a while to get it to connect properly.
In summary, while we had the regular amount of small questions, this was quite a straightforward system to build. There are far fewer components on this microscope for the user to assemble than on other systems. It results that the build requires simple tools and techniques, and all of the hard jobs are already done at the factory.
First Runs and XYZ performance
For our tests, we used a Hamamatsu Orca Flash 4.0 generously loaned to us from Hamamatsu. Connecting the camera to the microscope did demonstrate that cameras with a larger body would have a tough time fitting into the microscope access location on the sensor connection. We brought this to Zaber’s attention and were informed that they offer a riser kit for larger cameras, and can support cameras with large bodies.
Camera connection area. Note the LED illuminator cube directly above the camera. Larger bodies will require a riser kit supplied by Zaber for mounting.
Motion performance on the system was as expected. The XY stage uses a standard setup of lead screws and stepper motors. The focus/Z drive uses a linear motor, which supports fast operation, high accuracy and repeatability, but at a higher cost of components. I think it was a good decision to use a linear motor with the focus drive, and would love to see Zaber add linear XY to this microscope.
The control over the microscope can be performed using an included joystick, the Zaber Console software, or a Micromanager driver. We elected to first configure things in the Zaber Console to confirm proper operation, then to set up MicroManager for automated capture. Micromanager’s driver is a bit confusing to link up between drivers (you have to determine what controller and axis are operating a given function, 3.g. Controller 01 Axis B might == the Filter turret changer). But once things were configured, we had zero communication issues with the driver. Below is a video captured demonstrating the speed on a repeated XY move using MicroManager MDA for control.
Config window for Zaber Console.
We used MM 2.0 Gamma for our testing. A demonstration of the XY motion can be seen in the video below. This example included large Z moves and multiple channel settings to better visualize the speed of channel switching and Z stepping.
Initial samples used were a quite beat up kidney section, to demonstrate typical fluorescence performance. The objective we added to the system was a Zeiss 40x without UV apo correction, so some Z shift in color is apparent. Field illumination gradient was adequate, overall image field to the camera was well covered. This camera is a great tool for such testing as almost the entire 25mm output from the tube lens can be captured.
Collection of Z stacks for PSF analysis was straightforward. For these tests we used typical tetra-speck bead sets from Life technologies. What I was interested to look for here were coma or aberrations due to off-axis construction, none of which were observed. The system appears to be stacked up squarely, which was great to see.
40x PSF in Z/X40x PSF in ZY, note slight angular shift due to my failure to level the stage insert before scanning.
To analyze the repeatability of the XY stage, several locations were saved on the bead slide, and then imaged in XYZ using MDA with timelapse. The resulting locations were then projected to produce a single image. Results showed repeatability in all axes within Zaber’s specification. The GIF below shows total drift over several hours. Note the stage is moving away from and re-visiting this location. Z drift from thermal is also evident, but to be expected without an automated focus tracking mechanism.
Single location timelapse of beads under 40x magnification.
Z stacks captured in a similar manner to the prior experiment demonstrated even better Z performance, due to the employment of a linear motor stage on the focus axis by Zaber. Here, a single section is scanned multiple times in Z. The timelapse of these scans is stacked, so that numerous re-scans on a single set of images represents the same location scanned over time. When projecting this scan orthogonally, variations in Z will be visible. While expecting some linear shift due to thermal, there is almost no “wiggle” in the Z axis, due to the linear motor being so precise.
LED Performance
To test the LED performance we wanted to target two areas: field illumination performance and linear intensity regulation. Testing both can be somewhat tricky as almost everything will bleach over time. I used the blue isolation region of my bead slide, and it’s white label, to capture 2 multichannel timelapse series. Overall field analysis of each channel was then graphed to demonstrate intensity regulation. While a very small spike was observed in the UV channel, all channels performed considerably well, and it appears intensity regulation is well handled on the drivers for these LEDs.
Intensity plot on blue section of Life Tech slide. Channel intensity looks linear. White label region of bead slide. Decay rates for all channels look good, no major deviations caused by LED regulation, aside from a small UV blip at the start.
Field uniformity was great for a built-in LED system. This is always something tough to work on in a short-pathway LED excited system. Performance on multiple surfaces looked quite good. Some clipping can be seen at the upper left, due to camera placement. All channels showed this as well as a simple flashlight illuminated above, indicating this was due to my mounting and adjusting of the camera, rather than an excitation-side issue.
Blue region of bead slide, pseudo-color spectrum applied to better visualize intensity flatness.
Further Observations
Zaber added a drop/refocus feature to the microscope, similar to an escape function on a traditional scope. Using the linear motor’s speed, it is quite a fast shift to go from escaped to “in focus”. While this demonstrates the speed of a linear motor system, I would take care as an owner to know if I were “escaped” or just assuming so, for if a sample were placed over the objective, and the system to “return” at such a high rate through the sample, I imagine damage would occur to the sample or objective, or both. At the same time, this demonstrates the capability of such a motor, and slowing motion down in firmware/software is easy, while speeding things up is hard!
While Zaber did a great job with the included LED illumination, I can imagine customers would also benefit from using a LLG-coupled or fiber coupled light source. 4 channels is adequate, but many clients need greater diversity in channel selection, and stuffing more than 3 LEDs into an excitation module on-scope can be tricky, so I hope Zaber offers this as an option in the future.
The use of a linear motor for Z shows how great this motion method is for fast, reliable positioning. If Zaber were to add an autofocusing system to this axis, it would provide a nice improvement in market applicability for timelapse observations and high speed high magnification scanning. Similarly, the option to purchase a linear-motion XY top plate would be great, for those clients needing high speed scanning of a large region.
Summary
I really like this microscope. It has the feel of an industrial motion system adapted to an optical platform, which makes sense considering its pedigree. I can imagine that this would make an excellent choice for a plate scanning system, would do well coupled to an incubator, or would be a great fit for commercial clients working on automated analysis of a product, reagent or similar project. The addition of an integrated autofocusing system using reflection would greatly expand the use of this scope into timelapse live-cell work, where it’s shape and design would be a great fit for an incubation enclosure.
Customers who would do well with this microscope are those with some technical chops, who also don’t want to hand-build a microscope due to time constraints, or commercial customers who need a no-frills motorized microscope for scanning. As a company, Zaber has always provided great technical support and has a history of building precision motion systems at fair prices, so I would definitely recommend considering this system if you are in the market for an automated microscope.
-Austin Blanco & Garrett Bunch
(Disclosure) - I was not compensated for writing this review, and my observations and commentary are my own. - AB
Here is a quick example of using the RANGE controls in the Triggerscope GUI Application, as well as an example of saving ranges to the on board SD Card.
We’ve made a new video example of how to get things set up on the Triggerscope with the “Micromanager” version firmware from Nico. Please take a look if you are interested in updating your Triggerscope to use this code, or if you want to learn more about using Shutters, blanking, and presets for the -MM firmware device.
Recently one of my clients was working with a Blackfly S camera from FLIR, and noticed that the TTL signaling was not working properly. With some investigation, we discovered the cause to be the camera running at 3.3V output TTL, with very little drive current, whereas the Triggerscope is configured to accept 5V input TTL signals.
Needing to address this problem, we used a standard level shifting circuit, and stuffed the wires into a small enclosure. After thinking about this, I figured others may have the same problem (not only with PTG or FLIR cameras, but others also), and so decided to roll out a dedicated PCB to address this need. So – it’s posted to the store website. The circuit diagram can be seen below for those interested. You can place orders for these on the storefront here, with shipping as early as the week of 10/12/20.
This can be used with any device that outputs a 3.3v signal. If you have questions on how to connect things or if it will work for your system, please don’t hesitate to contact us! – Austin
I’m excited today to announce the release of the Triggerscope version 4. TG4 marks a major improvement in the performance and capability of the Triggerscope.
New Features
At the heart of Triggerscope 4 is a New high speed MCU running @ 600 Mhz. This is an 83x improvement over the Triggerscope 3B.
On board 1024K MCU RAM provides more than enough memory for arrays.
A new features provides access to a 16GB External SD Card, installed inside. Memory may be used for storing data for sequence access, recording of external parameters and timing events, or saving of advanced settings.
A new Real Time Clock is included for better timing over long duration experiments and delays.
DAC update rates can be overclocked, to a maximum frequency of 270kHz.
Integrated and simplified external controls for easier operation.
New Software
In addition to the release of Triggerscope 4, ARC is introducing a python-based, multi-platform compatible standalone control application. Our application can be installed on Windows, OS-X, or Linux systems. Source is also available from the GitHub Repo here. Users have two options for use – EXE and APP executables provide a small containerized version of python, so the entire application runs without any external installs required. Or, for customers who already have python installed, simply downloading and running the native python file is an option.
For debugging, all communication between the software and the triggerscope are printed for the user to view, to make diagnostics and custom driver development as simple as possible.
Light and Dark themes are provided to keep monitor glare down during imaging. This software is available for all Triggerscope 3 and up devices, and can be found on our GitHub Repo here.
New Micromanager Firmware Options
Nico Stuurman recently undertook a huge endeavor, and implemented a new approach for using MicroManager and the Triggerscope, with faster syntax, greater memory capacity, and tight integration into the Micromanager sequencing system for fast device control. ARC can install this firmware option before your triggerscope ships, just let us know which version you’d like to use!
Thanks to some generous industry friends, I finally managed to get my hands on a seemingly unobtanium RPI “High Quality” camera. I’ll have more info on the camera itself regarding performance, but my first question was – “can it be effectively cooled? ” Fortunately, having run similar experiments on a Point Grey / FLIR camera, I had most of the components and a basic test method ready to go to figure out the answer.
To start, we simply piled up thermal tape on the backside of the camera. This provided a poor but useable thermal coupling to the back of the camera PCB. Ideally, we would wrap the entire camera system in aluminum, but for now, this works. Next, we used a off the shelf TEC, and a CPU radiator, for the heat exchange.
The camera sits atop a TEC, which sits on an aluminum block, which sits on top of a CPU cooling sink.
To test performance, we obtained 40 images with an exposure time of 5 seconds. We only ran the TEC at 1V / 125mA. While running the experiment we recorded an IR video to document the reaction. What is quite evident at about the halfway mark, when the cooler is enabled, is that the TEC Cold side goes “dark”, and shortly thereafter the aluminum C mount housing of the camera as well as the exposed PCB begins to cool down. Images obtained showed corresponding drops in background intensity of ~ 10% for this test. Not amazing, but the drop in mean image intensity directly matches the enable and disable of the cooler. Further tests will include a tightly wrapped enclosure to better thermally sink the complete camera sensor cell and PCB.
A drop of ~ 8 counts can be seen after the cooler is enabled. Once the Cooler is disabled at ~ frame 24, the mean continues rising.
Of additional interest is the noise in the image from the readout taps. Of the images obtained, a clear pattern can be seen, again with the lens cover on and exposures of 5 seconds. A bloom can be seen on one side. I’m curious how this may change with a better cooling system. Below is a pseudo-colored maximum intensity projection of the 40 frames obtained during the experiment.
A basic example of read noise on the taps can be seen by looking at the standard deviation over the frames. This isn’t perfect but it does show a general amount of error in readout. Performance here was not bad at 3 counts maximum change over the sensor field.
As with all such tests – further study is needed :-). We plan on taking this camera through it’s paces in a lot more detail – so – more to come soon!
All over the world people are being asked to work from home…
Yet how many of us have had to do so for extended periods of time? As a case in point, are you reading this now while sitting at the office? Or, worse – while sitting at home, when you should be working? If so, this guide is for you! I also have experienced this challenge, but have had the opportunity to refine my work procedures while conducting business at home for the last 20 years. So – if you are working from home today, or plan to do so in the future, I hope these tools will help you maximize your enjoyment and impact while away from the office. The following sections I hope will give you clarity of purpose, the proper mindset to work alone, a set of practical tools to work alone, and finally, a method to evaluate how well you are doing at coping with this change.
Preparing the heart and mind to work alone
To be free to operate independently is a privilege. For most people over the course of history, employers or overseers would not or could not trust those they watched to “work hard”. As a result, work was “managed”, typically under brutal forms of motivation. Of course, there were notable exceptions to this. In the New Testament we find Jesus using a story of three servants who are given large sums of money, “Talents”. All are given rather large, but different sums of money (roughly, 1-3 years’ wages), and told to use the money for the masters’ benefit. Two of them do so, realizing a gain, while the third, buries the money. When the master returns, the two who have profited are rewarded with further authority. The third returns the original sum, saying, “Master I know you are a hard man, taking what you did not earn, reaping what you did not sow, and so I was afraid and hid the money, so here is your Talent back.” But the master replies, “You know I was a hard man? At least you could have put the money in the bank and earned interest!”. The servant is then fired. This to me is a fascinating story. It tells us so much about how life was 2,000 years ago, and what we can basically see is that not much has changed today. Leaders of companies may be tough people, oftentimes we will find ourselves questioning the morality or fairness of the decisions they make. Some wrestle with a love of money so intense that they will allow others to be hurt, so that they can gain further wealth. At the same time, we can see that those of us who use resources wisely are given further trust – and can we not see this principle applies today? If we at our work prove ourselves capable and responsible with the freedom and authority we are granted, most of the time, we will be offered greater freedom and authority. Now of course this is not 100% of the time – when it isn’t, I’d suggest the management is not doing well – as this principle is a simple, effective and fair one for any organization. So – whether by promotion, a change in work policy, a change in life situation, or even a global pandemic, here we find ourselves with this new authority – the authority to do what we want, when we want, and with no one watching over us. So what will you do with this new authority over yourself? The question itself is defined by one word: Integrity
In the Marine Corps, one of the principles drilled into our heads was that integrity is what you do when your drill instructor isn’t there. Similarly for us, integrity is what we will do at home when our management, more importantly our team isn’t there to motivate us and keep an eye on us. So these stories convey operational principles and the question of our own personal morality. We all must ask ourselves if what we are doing is the Right Thing. So, here are some thoughts to keep handy while working, or in case you find yourself browsing facebook during work time:
YOUR COMPETITOR IS WORKING HARDER THAN YOU RIGHT NOW If you don’t work hard, keep in mInd the people who you compete with. They are likely also at home – and if they are working harder than you, at some point this energy difference will result in your company losing it’s position, resulting in you losing your employment. This is harsh, but I think we can all agree rather obvious.
DISCIPLINE PROVIDES OPPORTUNITY AND POWER If you do work hard, you can realize the personal joy and pride of knowing you did well for yourself, your team, all on your own – further, you can grasp the power of your discipline, knowing that you can work on your own in any other job! This opens up a massive new world of employment opportunities – as there are quite a few people who simply cannot discipline themeselves! So you are more capable, a better team member, more employable, and ultimately, have greater freedom as a result of your discipline and efforts.
YOU ARE NOT A THIEF – SO DON’T STEAL. If you are being paid to work, and are not working, you are stealing. Not only from your employer, but from those members of your group who ARE working hard while you don’t. You may not consider the owners or management worthy of your integrity, but we should all consider our peers as deserving of our best. Get after it.
Practical tools for working at home
Prepare yourself
For the next few months – keep your regular work routine as much as you possibly can. Get up and dress in your work clothes. Do whatever you need to be presentable and prepared for your job. Eat breakfast as you normally would at the same time. All of these activities will help mentally set the stage to understand that “We are now working”. I know it seems wasteful – but the mind needs this routine, especially when so many changes are all around us. Bear in mind, your work commute now takes 3 seconds, and traffic is always light!
Prepare your “office”
My office in 2002. Note the Ghost Recon game & IPA were NOT during work hours! 🙂 Our 700 sq/ft apartment was small, but I accomplished a ton of work from this tiny desk!
My first office was a piece of junk computer stand 4 feet from our kitchen in a one bedroom apartment (pictured above). From that little cove I covered a sales territory encompassing all of northern California for 2 years. In that time I attained a salesperson of the year award from Molecular Devices. But I MADE THE SPACE for my office, and when I was sitting there, even when the wife was watching tv 5 feet away, I was “at work” during business hours. Because so many of us find ourselves without preparation today, you might make your office be the kitchen table or even a folding table for now. But – wherever it is it should be away from the living room if possible, and in a place where there are the least possible distractions. In front of a window? Close it if it’s distracting. You can open it after you rebuild the routine. In a noisy location? Amazon prime a headset. But make the space, and remember that while you are there, you are “away at work”, away from the responsibilities of the home, away from the XBOX, away from the kitchen. Those things don’t exist, because you aren’t there – you are at the office!
Prepare your schedule
As you are now your own boss at home, you will probably find it hard to stay motivated, as until there is a deadline, do I really have to do this now? Yes you do! Using our calendar, block out time for each project as you need. Make sure to include a 15 minute break every so often, as well as your lunch break. This is helpful as when the desire to check Instagram hits – it’s better to have an alternative – e.g. “Well I only have 2 hours to finish this data entry project, so if I hit instagram right now I won’t have time for the job”, instead of “Hey let’s go see what’s up on instagram, there isn’t anything pressing at work right now…”. The difference in mental position is amazing.
Prepare your family
Kids and the spouse may find it tough to understand why they can’t pester you while at home. This is very important to draw a line while working. If they are interrupting you while at work in the house, they are literally taking food from their own mouths (is your competitor allowing such distraction? No? Then you are losing right now!!!). Your work is important, and they must honor your endeavour. This simply takes training and repetition to realize for them, but give it a few days and they will see your clothes, you sitting at the office, and soon realize, “Mom is working right now, I can’t bother her”. Now – I should note that one of the greatest joys for me is allowing my boys into my work life. I’ve had them help with many work projects, learning along the way. Over the years we have developed a system where they will visit the office to tell me stories about school, ask questions on things etc. But at first – the barrier must be established for your benefiet as well as theirs. If you allow distractions now, they won’t respect your requests later for peace and quiet. Further, what are you telling them about the value of your work? So have the family meetings as many times as are needed, and keep up the barrier for the short term. In a few months you can experiment with opening that up – but this is a tough change for you – so minimize the number of fronts you need to be fighting on at the same time!
Prepare your management
Any time we are suddenly gone from the office, management can have trouble. People in leadership positions can have greater fear, greater uncertainty, than those in operational positions. So as bad as things may be for you with this change, it’s worse for them! Further, while you are struggling with how to cope with the change, they are doing the same, but also struggling with how to handle the managerial/directive changes needed to keep things going. In this time of chaos, you can be the stable anchor. This requires some creative thinking, good communication and diligent follow through.
Get the tools you need. This is critical. If you do assembly work, check out or record the tools needed from the office and take them home. If you need a soldering iron, buy one. If you need to have supplies shipped to you or you need to have a monday pickup / friday drop-off, talk with management and set it up. Ultimately there is a way to do your work anywhere – it might not be optimal, but it is possible. Be creative and solve these problems for your management, so they can worry about others and not you. .
During online meetings, write down the tasks you are supposed to accomplish, and then review them with the team or leader at the end of the meeting.
Share your online “self-schedule” with your management – this can be a great way to help them allocate resources. It’s much better to have a conversation where you say, “Hey I am trying to maximize my work in this situation, so I’ve cooked up a work schedule for myself. Please take a second to look at it and let me know if you want anything changed.”. If they see this, and have half a brain, the reaction will be “Wow, his employee is good to go – and I’m lucky they are so self reliant!”
If you are running out of things to do at home, spend some time thinking up new things you can do to help the team. Brainstorm with management – This is quite important because ultimately, if you do run out of things to do, why should the company keep paying you? With enough creative thinking and hard work, you should never end up with nothing to do.
Conclusion
I have set a rather strong tone on this subject. I have done so because initially, it takes a heap of effort to think differently about your work. But what also needs to be understood is the amazing freedom, efficiency and joy of working in isolation. How long is your commute? 30 minutes? You now have 5 hours back in your life, 5 hours. That’s almost a work day! What can you do with 5 new hours in your life? Learn a new skill? Spend more time with your family? This new time is a gift, and the only loss is the auto company and gas station! Learning to work this way makes you exponentially more powerful and employable. If an employer can see that you are capable of working like this – will they really question you when you ask for greater autonomy? Further, when you do meet in person, your meeting time will be more valued, and you will find greater joy in sharing time with colleagues. The richness of doing work together will be realized as now, it will be rare.
As with all things in life – today can be a chance for us to shrink from what we are called to do, or to rise to the challenge, and grow as a result. But having tools helps in our growth. I hope some of these tools help you in learning to adapt to this new work environment you may find yourself in. Good luck! – Austin
For some time now I’ve been using 8020 extrusion for quick prototyping of optical assemblies. It’s great for assemblies which require longer focal lengths and larger elements. For such systems, the choices are to use a breadboard or table, with posts – and then line everything up, having to worry at minimum about elevation and rotation of each element. Once lined up the parts aren’t quite easily moved around. For my parts, I simply created a negative profile for the “8020” 2525 brand of extrusion, then placed a 32mm circle at the center of this profile with vertical clearance. Likely I should have placed it higher, but for most elements it’s simple to create a clamp, send it to the 3-D printer, stick the element inside and voila, held at an axial center, generally en face, and very easy to slide back and forth.
For complicated systems which may use reflection or episcopic combined paths, additional pieces of extrusion can be cut and aligned to a core axis quite easily, and even attached in 3 rotations (left, right and “up” from the primary optical axis). Extrusion pieces can be ordered pre-cut, or easily cut to length using a hacksaw. Right angle clamps avoid any angular errors caused by bad cuts. Personally I use a mill to face off the ends, but most people don’t have access to a mill.
In this image I use the extrusion to align a large optic, with further parts out of frame.
To make things even easier, it’s nice to be able to mark off critical dimensions on the extrusion with a felt tip pen, which is easily later removed from the anodized surface with IPA.
In this example a high power excitation input was designed in Zemax to squeeze a bit more power from a fluorescent system. Before building the assembly the profile extrusion was used to verify the field collimation and flatness at the desired focal length.
I’ve added all of the designs I frequently start from, in STEP format. If someone needs another format please let me know and I’ll export one.
A few months back I was working on a custom microscope that required several sections to be aligned. The camera to be centered on it’s axis and aligned to the objective, the excitation wide-field illuminator to be aligned to the back aperture of the objective (and for that alignment to be coaxial), and finally, a laser source to be aligned into the back aperture as well.
Before the on site work, I decided to cook up a little “starter” jig, that would screw into the objective threads, and easily identify whether the laser was in fact coaxial. It worked fairly well, so I figured I’d share the model for anyone who wants it. You can find the f3d, STEP and STL files here on Github – Note the threads modeled work decently, but are my own mod job off of another fine pitch close-ish thread. They worked great when printed using my Prusa MK3, so I figure most people using the model should have no issues. I’ll probably make one for Olympus RMS threads when the need arises.
Over the past few years, I’ve often battled the Micromanager MDA window, when needing to perform high speed triggered acquisitions. While the system works well for multi channel Z stacks, running timelapse 2 channel streams, or “Z first” streams, didn’t work well. To overcome this, I’ve written a script that pulls all of the MDA user settings out of the window, loads up the Triggerscope, and captures the sequence.
This approach gives any user of the triggerscope far greater control over how sequences are run, and offers users the ability to customize external device commands if needed.
I’ve cooked up a brief video overview here, with some example screenshots of the results on an oscilloscope below.
If you’d like to use or check the script out, it can be found on my GitHub site here.
Please note this requires updated firmware (V 600 or up)
A basic example of a Z stack in a single channel is shown below. In this configuration, 1 channel is selected in the MDA window, and a single Z stack is collected. The Yellow line indicates intensity of a laser or LED on Ch1, the pink line indicates the Z voltage output, and the blue line indicates a TTL input from the camera.
In the next example, output from a “channel first” Z capture is shown. Here Channel is prioritized, so the system runs Ch1 , then captures all Z frames, thens witches to Ch2, and captures all Z frames.
Next, is an example of a capture previously impossible in MM. In this capture we stream 3 time loops back to back, with no delay.
Next up is an example of a “Z First” capture, where all channels are acquired for a single Z position.
Finally, a multi channel example can be seen in this image, with 2 channels running in a time series.
Those are the highlights – I hope others find this useful!
I frequently build parts, both aluminum and 3d printed, which are used with thor components. Using Fusion360 from Autodesk, it’s simple to add threads into a hole, or even create pre-threaded holes in objects. Luckily, Fusion360 even includes a C-Mount thread option.
But – the SM1 thread from Thor is another matter. I had to add one to a part, so I found this nifty trick in fusion which supports adding custom threads to your install.
It turns out Thor provides the required information to form the threads, so using this page I was able to pull in the thread settings, and generate my own thread selection.
For anyone who just wants to use the threads in their copy of fusion, please find the file located on my Github page here.
This is a great example of using Arduino in the lab. If you have limitations to your Lab hardware, and want to explore how to expand or modify it, please get in touch, as this is what we do!
Like so many who live in the sciences, I am fascinated by all things new, unknown, or barely discovered. I think some people just have this innate sense of a continued drive to understand, to improve our awareness and knowledge in the world.
Yet for many, the financial or temporal obligations of higher education aren’t possible to accept. Sure, there is night school, online correspondence etc, and these frameworks are excellent sources of gaining credentials, and of accessing new opportunities in a career. But what if I simply want to learn a bit about making parts? What if I want to build a little trinket of electronics, or to learn a little bit about optics? Today, this concise/iterative form of learning is available to everyone, yet only a few I interact with seem to exploit it’s full potential. It’s the way I’ve learned almost everything I know and use today. It does have downsides, but these can be filled with proper guidance. I would call this form of learning “Project-based” in nature. So, how does one attend such a lesson?
The Jellybox is a 3D printer kit you can build with your kids. (https://www.imade3d.com/)
Step 1: Take on a project in the field of interest
Let’s say that, like me you have an interest or a curiosity on how machines move. You’ve seen a 3-D printer, or maybe a robot, or a CNC machine, and wondered, “how does the table top move, what drives it? How does it “know” where it is?” All good questions of course! Now, I had these questions, and I never truly was able to answer them until I embarked on my first CNC construction project. This began as a kick-starter investment, and probably had a total cost of ~ $350 by the time I was done. It took 2 months or so of work to finish it completely. Spending a few hours here and there to construct it. From there, I tinkered and modified a bit, and finally, after several months of use, I ended up stripping it down to use for other projects. Now, numerous issues and limitations popped up during this process, and I also realized I was left with several questions. Which brings us to the next level of learning.
Step 2: Learn from the Experts
Some of the questions which gnawed on my brain at the end of this build were:
Was this machine actually capable of milling aluminum?
Why did the speed seem so slow?
Did I need liquid cutting fluid all the time?
How come these tiny dremel end-mills kept breaking?
What was the best GCODE generator to use?
These are questions which come not from the top level of a neophyte, but from a marginally deeper question of the enthusiast with some minimal experience. I moved from the neophyte to the enthusiast when I took on the project. I now had a surface level understanding of what questions to even ask! Not only that, but my ears itched for the answer. I HAD TO UNDERSTAND these answers, because my lack of knowledge was killing me, and affecting my understanding as to what this little machine could do! So I turned to people I know in the microscopy automation industry, gents like Chris Ballard from Sutter, John Zemek from ASI, and during the course of other work, would ask things like, “Hey so what exactly do you do with your machines to compensate for backlash?” Now here’s the fun part – no-one EVER denies an opportunity to share their expertise when prompted! So while I absorbed everything they had to teach, they were happy to share and to receive an opportunity to deliver lessons and experiences gained from years of effort. These small interactions may have taken 10, or 15 minutes, but over time I accumulated a series of data points. Some things like, “well, we always use fluid because we are cutting so fast” allowed me to understand that speed impacted heat to a greater degree than I had assumed, prompting me to search down google eggs like this speed & feed calculator. Other times, I’d learn objective known facts like Chris stating, “It’s hard to beat mass, when it comes to CNC, and microscopes for that matter, the heavier the better. ” Now such a statement seems simple, but because I had the background of watching my tiny machine struggle to cut, and had the framework of knowledge for that statement to fit, I quickly was able to understand the why behind the fact, which allowed me to cement a better understanding of what this meant for such machines. Vibration, strength, heat, inertia, it was all making sense.
This kickstarter campaign will provide classes on AI using openCV. https://www.learnopencv.com/
Step 3: Take the next class
How to proceed? Simple: Build a machine that supported my next level of learning! In this case, it was a used RF-45 geared head mill. Armed with my understanding of how motors drove my current CNC, I snagged a used RF45, and designed my own CNC conversion for it. My design was additive, meaning that even if it completely failed, I could revert back to owning a manual mill – and who doesn’t want a milling machine? 🙂 So the next level of learning, the next class, had begun. Through it I learned my motors weren’t strong enough, my motor drivers were not high enough current and too slow, I had to account for additional backlash on the bigger machine, and so the journey continued. I still use the results from that machine for small projects today. The experience gained during the project has been too enormous to measure as I’ve applied it to things like, “hey, you can’t make a box with square inside corners, because all end mills are round, so how will it be cut?”
How do I know I’ve gained requisite knowledge in a field? The answer is, I never have. At each level of learning I’ve discovered new and more interesting aspects of a field. Liner encoding, DRO’s, automated tool changing heads, variable speed control GCODE, a litany of CAM generators, new 3 phase motors and controller options. So when is learning a field enough? I don’t think there is an upper limit. And this is the most important principle in my humble opinion. Those of us given this gift of curiosity have an obligation to leverage it. In an era in which Khan Academy can teach you trig for free, there is no excuse to stay stagnant. More importantly, I have watched several colleagues declare an end of learning, and subsequently become irrelevant. From, “I don’t do email” to “I can’t understand programming”, these people made the choice to stop.
And the world kept going.
And they were left behind, no longer useful to the community they lived or worked in. So whether it’s art, philosophy, religion, sports, outdoors, history, science, or just learning about the lives of others, we must never accept a point at which we believe, “I have arrived”. And so what is the final exam? Well, it’s likely comfort. Are you comfortable in your work? In your technical experience? Then get uncomfortable. Engage in that arena you were scared to try. Try out Jiu-Jitsu even if you’re scared. Order that 3-D printer kit, even if you don’t have time to build it. Download Python and follow some online tutorials, even if you never use it again. Stay off balance. If you are comfortable today, you failed the exam. The good news is that you have another opportunity to take the test, and learn something new, staring today.
For a new Triggerscope 3B shipment, remove from packaging and account for the following:
12V power supply
Mini-USB cable
SMA-BNC connector cables, if purchased
ARC certificate of compliance paperwork
Triggerscope 3B Controller
Hardware Connections
Once unpackaged and all components are accounted for, plug the 12V power supply into the slot located on the left side of the unit labeled “12V,” and plug the other end of the power supply into an available power outlet.
Next, plug the mini-USB cable into the left side of the Triggerscope unit in the slot labeled “USB,” and plug the other end into the computer you are going to be using.
Driver Install
Next, locate the switch on the right side of the Triggerscope 3B, flip the switch either way, both ways turn the Triggerscope on. Open a new tab on your web browser, and download the Arduino IDE Software that matches the Operating System you are currently using. Follow the install prompts to install the software
With install of Arduino IDE complete, open the newly installed Arduino IDE application on your computer.
On the top ribbon, select the “Tools” tab. Then hover over the section that says “board” and then click on the “Board Manager” option.
Next, in the “Board Manager” window, click on the “filter your search” box and type “DUE,” and the following should pop up on the screen, “Arduino SAM Boards (32-bits ARM Cortex -M3) by Arduino.” Click install on this option.
The Arduino application will proceed to download and install the driver package needed to run the Triggerscope 3B unit.
MicroManager Setup
Most end-users will already have MicroManager installed, but if not, make sure to use the nightly builds found here.
In MicroManager, select the “Hardware Configuration Wizard”, Click Next until reaching step 2. In the lower list, browse to the “Triggerscope” section, and add the Triggerscope Hub Device.
For the Communication setup, select the COM # assigned to your triggerscope under the Windows Device manager, read as “Arduino Due Programming Port”.
Configure the Com # found int he device manager, make sure to set the BAUD rate to 115200.
When prompted, select the TTL and DAC lines needed for your application. Also note DAC 16 is tied by default to the FOCUS device. If running sequencing for Z stacks you’ll want to add this.
Continue through the dialog options, if connecting to a Z stage, be sure to specify the maximum and minimum height of your stage so that Z data is properly calibrated. Contact ARC if using a range other than 0-10V.
Next, confirm proper operation by opening up the Device Property Browser. You should have discrete control over the DAC lines added, and on/off state control over TTL lines. Note that the Triggerscope 3B will illuminate an output LED when DAC control is enabled, or when TTL control is enabled. This can be very useful to confirm proper communication with the computer.
This concludes the basic setup for Triggerscope 3B. Please contact ARC with any questions if you are having difficulty!
As client demand continues to grow , ARC has been looking to expand the team, and is pleased to announce the hiring of ARC’s first employee, Daymian Rocca.
Daymian joined the team as Technical Systems Engineer Jan 15th, and brings to the company experience in MSCA, fabrication, additive manufacturing and firmware development. His primary role will be hardware & technical systems , as well as supporting work in the software and optical areas we work in. Please join me in welcoming Daymian to the team!
I’m excited to announce the release of the newest Triggerscope model the 3-B. This version replaces the V3, and is packed with improvements for practical laboratory use, including:
DAC Software Range Selection
Range selection is now software controllable for each channel. This means you can get a full 16 Bit resolution delivered to your device in any range from -2.5/+2.5V, to -10V/+10V, as well as -5/+5V, 0-5V, and 0-10V. A demo video of this feature is available below.
LED Status Indication
When integrating or first using any TTL controlled system, it’s difficult to determine whether the controller is properly firing trigger signals, and whether the device is properly outputting changes on the TTL and DAC lines. New LED’s on the Triggerscope 3B indicate an active sequence, TTL status, DAC output status, and input trigger status, all from the face of the device. In addition, these signals can be disabled or enabled for compatibility with ultra low light acquisition environments.
High Current TTL Drivers
When driving Lasers, the 50 Ohm impedance used can cause a tough voltage drop problem. This has been addressed by now sourcing up to 500mA per line on TTL lines 1-4. In addition, lines 5-8 now source 200mA per channel. While most systems should work great at 200mA, the higher current channels may also optionally be used to drive low intensity LEDs if needed, for applications such as transmitted illumination, powered directly from the Triggerscope.
An External DC Power switch is now included for simple restarts.
On a recent project I had an opportunity to collaborate with some great manufacturers and vendors, to build a custom microscope for Dr. Chia-Yi (Alex) Kuan, at the University of Virginia School of Medicine. This instrument is quite unique, and required a team of manufacturers to pull it off.
Completed system ready for use.
Dr. Kuan required an upright confocal microscope, which could perform photoactivation, widefield and confocal fluorescent excitation, all while running on an extended focus throw of 2″ range. The system required several custom pieces of hardware and software, which made things extra *fun*.
This image was taken from a live specimen, showing cranial vasculature in vivo.
Team Contributors
Visual Dynamix LLC, headed by Gary Tockman, was the lead system integrator on the project as well as the primary service provider for the system. Gary led the team on the build and did an excellent job defining input specifications and performance criteria, as well as managing the crazy logistics of building a system from so many different vendors.
Using the same device for slides and for live specimens required some work on the focuser throw. Sutter Instruments provided a great solution via the BOB microscope. Chris Ballard spent a great deal of effort working out a long travel Z motor relying on the MPC control system for XYZ axis.
89 North provided the photostimulation system, confocal, and LDI laser excitation. Scott Phillips and Simona Stelea both spent several days on site working on the system to make sure everything was dialed in properly.
Scott Phillips works on cable connections
All of the devices on the system needed control via Metamorph. I worked with David Biggs over at KB Imaging to handle this part, and was very glad I chose his work. David has extensive experience with driver development, and due to the proprietary nature of the firmware on this instrument, his experience saved the day on dialing in the driver for speed and reliability.
Finally, I took on the system I/O side for lasers and triggering, as well as building the imaging PC and configuring Metamorph. Because the latest Triggerscope 3 model needed to drive the lasers,I also managed to work with David to create a Metamorph driver, so if you happen to run MetaMorph and want to control the triggerscope, please get in touch.
Gary inspecting the filters on the XLight
Systems like this usually require a day or two for the install, but in our case, most of the install team spent a week on site, to be certain that the details were ironed out and to get some training on the system in for the end users. In our situation this was a good call, as we found the inevitable last minute changes which needed to be addressed. Having the team together made addressing these things straightforward.
Results
A bit after leaving, the client sent over a beautiful video showing experimental data which includes the visualization of vasculature, with a clot stimulated by the laser exciter, and a resulting timelapse of that clot forming.
Training for end users on a live specimen
It’s great to be able to participate with clients, manufacturers and engineers who can pull builds like this together, and better still to watch this important and exciting research move forward. I’m even happier I get to share this build!
During a recent project for a client, I had to prepare a fluorescent bead slide for imaging. Beads require dilution, and a vortex mixer is recommended in order to provide ample separation of the individual beads. Not having one on hand, I figured there must be a way to achieve similar results, and found this used by a homebrewer for yeast prep. It was close for my needs, but I didn’t want to use wood due to the fabrication time and difficulty of install / removal. So I measured the screw hole spacing on the sander pad, and sketched one up in Fusion. A PLA print was made, and the result has been great for simple use.
One additional trick I use for mods like this, is a router speed control, available form Harbor freight or Amazon. It allows the motor speed to be adjusted. The little Ryobi is super fast, so I ended up suing the speed control on it’s lowest setting. These controls work well for most motors – some using “soft start” motors may not work, but it did great in this case!
If you would like to print your own (assuming the hole spacing is compatible), the STL file and STEP for modification are available on my Github page here.
Flir is pushing these new Sony sensors, along with Lucid, for use in remote sensing and inspection. These are interesting.
Basically each camera can capture 4 polarization states in one image. I can imagine these may be used for several microscopy applications, chiefly in polarization light microscopes, but also in DIC, and stereo applications where specular reflection is prevalent.
The resources below are for students attending my drone courses at Norcal Flight Center, but if other readers stop by, I hope you find these useful!
The FAA classifies certification for commercial use of drones as an “sUAS” cert. Or, a small Unmanned Aerial System, Remote Pilot certification. This certification allows us to operate a drone up to 55lb, for profit, in much of the US airspace. Below are links and resources, as well as questions and answers that come up during classes. Feel free to post here with more questions if you have them!
This is for part 107 operations, or sUAS operations.
If you are having trouble with reading of charts, especially the Lat/Long stuff, here’s a great video that walks through the steps.
—-UPDATE—-
Some answers to the questions which came up during the class:
Question: “Can a rPIC certificate holder operate within 5 miles of a non-towered airport?”
Yes – refer to FAA AC 107-2, section 5.8.1. “…Unless the flight is conducted within controlled airspace, no notification or authorization is necessary to operate at or near an airport. ” (Applies to certificated sUAS pilots)
Question: “Are sUAS operations permitted in MOA’s?”
Yes – There si a great study table on airspace from this website, search for “MOA”.
I’m excited to share the following publication from my colleagues at Neurovision Imaging & Cedars Sinai Medical Center. This paper represents a ton of work, from people all over the world. I’m also happy to say I had a chance to play a very small role in supporting the efforts!
This research continues to advance the work of attempting identification of Alzheimer’s via the retina. If we can continue to refine this approach, someday, people will be able to have frequent checkups to determine whether they are approaching a risk of Alzheimers – early enough for intervention to occur.
Heat map example of AB plaque identification
For the human trials, images were obtained of the retina, using a custom modified confocal ophthalmoscope. The retinal imager obtains images from the patient’s eye, and the images are then analyzed for a number of potential plaque sites (those sites which may contain AB plaques). If enough sites, and or site density is found, the patient indication shows higher, whereas a control would show less grouping and/or less sites. This is a simplified explanation of course, and a ton of work went into figuring out how to best identify these sites. Here’s an image of such a patient. Int his image the heat map indicates the grouping and intensity of the AB plaque locations.
Hats off to Maya & Yosef Koronyo, the team at Neurovision Imaging, and the folks at Cedars for this awesome work!
I keep looking into a low cost, yet stable way to generate nice sine waves which are controllable, using something other than a signal generator or one of the cheap breakouts which never seem to work that well. This led me to considering audio systems as a possible source of signal. It turns out that the iPhone app store has a nice little tone generator app – aptly named “Signal Generator“. The app has a frequency range from 100Hz to 20Khz. Connecting the output of this into an oscilloscope shows a really nice signal. I worked on buffering this through an op amp, and sure enough, it works great! So, could an enterprising person use an old iPhone as a driver for a galvo…? If anyone is interested, I can send over my inverter+amp design for you!
I made a short video showing the results – I hope someone can make use of it!
So i finally spent some money on a decent site theme. I hope you like it! If anyone experiences any issues in using the site with this theme, please let me know!
Do you build systems which use Arduino or Raspberry Pi boards? Are you happy with the enclosure options available today? I’m not either. But I’m having some trouble figuring out the best possible products to offer. So, I figure there’s no one better to help than the people who need such products. Would you help me out by filling out this very brief survey? It’ll go a long way in helping me find the best path forward in offering a next-level enclosure for our community!
It appears that more and more people want to use PWM control for illumination devices from Micro-Manager and other imaging software. PWM may be used for any number of applications, from high speed pulsing of an LED, or a laser, in order to reduce phototoxicity or just to control brightness, or to drive a DC motor at a varying speed, or to drive a device like a spinning disk to set the PRM. I figured I’d address this using the Triggerscope system controllers. rIn order to support PWM drive over an external device, I wanted a few useful functions to work in MM:
PWM duty cycle should be controlled form presets
PWM should be called to “off” from a TTL or other “shutter” style command
Once off, a similar “ttl on” type command should re-enable PWM at the alst used duty cycle
multiple output lines should be supported at different duty cycles.
Version 407 of the Triggerscope firmware now supports this, and uses the existing driver available for these devices. I’ve made a short demo video showing how this works on an oscilloscope output. I’ll place an option for this on the store. Please get in touch with any questions or post here – thanks!
One of my recent projects which was very exciting and interesting was to build a custom imaging system for John Mclaughlin at Torch Therapeutics. This was a great build for a number of reasons, one of which is that Torch has allowed me to write a report on this build, which is greatly appreciated! From the tiny camera to similarly tiny NUC computer, this was a really interesting build, and I’m excited to share what I found during the testing and setup of the system. If you are looking for this type of custom integrated system, please take a look at what my company offers, as we’d love to build a system for you!
Scope Selection
What we were looking to build on this system was a low cost, yet fully automated imaging scope that would be easy to modify, simple to operate, and compatible with Micro-manager. In the short term, only Z control is required, but as the work grows, we wanted provision for XY automation, as well as autofocus tracking. For fluorescence excitation we an LED illuminator. After looking at several options, we selected the ASI RAMM microscope, with the inclusion of the Tiger unified controller, and the ASI LED excitation module. This system offers a complete microscope from one control box, on a scalable build platform, at a competitive price. I reviewed the RAMM scope a few years back, and happy to see that the quality and options have only increased over time. When I reviewed the system, it was required that I build the frame and align things correctly. The new systems ship completely assembled. I literally pulled it out of the box, plugged it in and things were operational. This out-of-box experience isn’t normally seen even in the “big 4” microscopes.
RAMM scope after unboxing
Dual lightpath setup for focus tracking – dichroic for epi on the left (thumbscrews shown) and provision for IR cut mirror on right.
Another feature of this scope is the inclusion of all needed driver components in one box, ASI’s Tiger controller. This is a modular control box which can accept riser cards as-needed to drive various components. The controller on this setup was actually the largest electronic box in the system! From left to right are installed driver cards for joystick/control input, Z stage, LED output, and filter wheel control. Another great feature of this box is that when installing in Micro-manager, only a single USB connection, and single hub device are required.
Tiger Controller, with intel NUC on top
LED Illumination
ASI offers a 4 channel LED illuminator, with option for almost any available LED module. This is a simple illumination setup using a common ladder-dichroic design. The open nature of the hardware allows for changes to the dichroics, or the LED modules, as may be needed by the customer as things change in the future. Each LED is driven using a simple audio style TRS cable, so connecting or disconnecting the LEDs from the driver is straightforward. On the output side of the module, an aperture diapragm is provided to avoid overfilling the back aperture of the objective.
Camera Selection
When selecting a camera, we wanted good QE, decent resolution, but didn’t require any advanced cooling or long exposures. Of the available options, the Pt Grey (FLIR) BlackFly camera fit the bill. Recently, Nico Stuurman @ UCSF wrote up a driver to support this camera in Micro-manager, and after working with it for w while I’m quite impressed. I was able to configure some tricky stuff, I tested various binning modes, subarrays, a wide range of exposure times, and things seemed stable. One suggestion if using this camera is to always snap an image after making changes, vs. simply clicking “live”.
The camera is unbelievably small, roughly the size of a 1″ cube. While cool at first glance, there are some drawbacks to such a design which I note below. I tested the camera at no-light conditions for 2 things – dark current over exposure time, and read noise. Read noise shows a 16-bit count standard deviation of 214.78. Value ranges on the noise floor ran 3264 counts max-min. This works out to a noise level of 4%. Calculation for this measurement was from 2 images in a sequence.
(Image1+2000) -image2 = 200 count centered noise level. (ranging around the 2k level).
Not the best performance from a typical sCMOS camera, but if we consider the next lowest-cost camera runs ~ $5,000, this is quite good in my opinion. There is some pattern noise apparent in the camera, below is an average of 20 exposures, all using 10ms exposure time. The image has been contrast enhanced and pseudo-colored for presentation.
Average of 20 images captured @ 10ms exposure time.
So it appears the taps are drifting a bit. Just for grins I tossed one of these images into an FFT and redisplayed the spectrum for view. Looking at the output, my gut says the image below results from temperature bias on the output taps, and this bias is distributed across the back side of the sensor, or at least wherever the taps are located on the readout layer of the PCB. The higher frequency events at the center look like the typical clock timing jitter seen on any ADC. But this is only my non-expert observation – I’d love for any uber-camera experts to weigh in!
I also wanted to look at how bad the hot pixel effects would be using longer exposures. For this test I ran a set of exposure times from 1ms to 3000ms.
Increase in dark current over time was about as expected.
I think the bottom line on this camera is that it runs as hot as any other camera, but has neither the active cooling nor the inherent surface area to radiate heat well. I took a pic of it using my Flir One camera, and it runs at about 95°F while idle.
Does this mean the camera isn’t suitable for microscopy? Not at all? This is an amazing piece of tech for a very low price. I can imagine buying 3 of these, one for each of 3 emission channels on a single scope! My goal in presenting this information is to share what the current limitations are for such a product. I think the raw QE and ~2.3MP resolution of the camera make it a perfect fit for most microscopy jobs. Of course, there will always be need for higher end cameras, but for many run of the mill operations, this is a nice solution.
NUC Computer
When searching for an “imaging computer” on this project, I had initially considered using a Mac Mini, dual booted with windows 10. I’ve used this for a number of other projects, and it has always run well in windows. John suggested looking at the NUC as an option, which provided later opportunity to upgrade the RAM and disk space. After building it up (which only required installing memory and an SSD), this little guy kicked butt!I ran Windows 10-Professional x64 for this build, and used the latest version of Micro-manager. Funny that a $500 computer and a $500 camera can be had for what used to run ~ $15k!. I successfully ran this on timelapse for 10 hours, and captured streams in MM of 100 frames. I didn’t push the buffer too much or analyze the USB-3 performance, but overall this is a great little machine for simple capture of images.
Building this system was a lot of fun, and I really enjoyed using non-traditional components for it. I think this type of system will become commonplace in the future, as more and more customers realize that traditional components, at a traditional high cost, aren’t always the best fit for their needs. If you are interested in this type of solution for your lab or company, please get in touch, as I’d love to build one just for you!
Micro-manager guru Kyle M. Douglass recently posed his implementation of micro-manager on a raspberry Pi 3. Very cool potential here, considering when the computing power of the pi is exceeded for a given application, one could just add more for $45!
I’d imagine that memory handling issues related to image capture would be the biggest problem for the rpi, but it wouldn’t be surprising to see that addressed in the future. It looks like accessing cameras such as the point grey chamelion has been accomplished, however over 1394, not USB.
While there are a few viewing tools available for OSX, I’ve been looking for something that was higher quality, and more configurable. Today I stumbled upon Cuprum. This viewer supports layering, export of user-configured views, some good print options and other stuff. It’s $13 on the Mac App store, and well worth it IMHO.
Here’s an example of one of my breakout board shields. Overall this makes review of a gerber output MUCH easier than other programs I’ve tried. An app store DL is available here – It’s $14,99 on the app store.
As the 2020 FAA mandate for ADS-B comes upon us, more aircraft are using the ADS-B system. Additionally, weather transmission via towers is a major free source of in-flight weather info. Having recently picked up a new iPad, and subscribing to FireFlight, I decided it was time to add the ability to see ADS-B traffic, and snag weather.
Having done a bit of homework, I knew there were some open source solutions available, so of course that’s the way I was going to go. Heck I even considered repurposing one of my other rPi’s for the job, but meh, better to dedicate a box for it!
With a flight coming up where I wanted the weather, I decided I wanted to get something to use NOW. Amazon same-day-delivery to the rescue! Here’s what I bought:
All in I was @ $120 for the setup. Consider that the closest commercial product runs 3 or 4x more!
So this must be trouble to set up, right? Anything but! Upon recieving the components, I had the system working in ~ 8minutes! The work required is to:
install heat sinks on rPi IC’s
install rPi into case
insert microSD card
insert USB tuner(s)
insert power supply USB
plug in
connect on the iPad.
Unbelievably simple! This couldn’t be any easier for a “maker” project. In the pic below you can see the antenna I hung in the window, the case and tuner, and the iPad with the Stratux host page open. I experimented with using both receivers, and each receiver solo, and found that using 2 receivers really improved the # of detected 978Mhz signals. Not sure why, but I’ll take it!
SO I’ve been working with AutoDesk’s Fusion360 for a while now, and have found it to be an exceptional tool for diving into CAD. If you’ve considered CAD before, but have been scared off by the learning curve, I recommend checking it out. One of the important functions of a truly parametric CAD program is the need to reference objects to other objects, and to reference measurements to variables or other object measurements. I knew Fusion360 could handle parametric work, but hadn’t been able to figure out a solution to my particular problem, so, here’s a video on how I did it. Not sure if this is an accepted method conventionally, but it worked for me!
The problem I had was how to set up a reflection line, which was dependent on 2 inputs, the angle of an input source, and the reflection angle of a mirrored surface. I wanted to be able to drive these 2 input values, and have either of them affect the resulting reflection line. Here’s how it worked out.
I wrote this for a client, but figured others could make use of it. This code simply captures a number of images as defined by the user, and saves them to the specified folder without displaying them. This is useful if you don’t want all of the images open in memory during a timelapse.
I can’t believe I missed this excellent post from Sam Lord @ Everyday Scientist on how to insert an emission filter on your ocular lightpath. Having been hit by some untold number scopes wherein I either was observing, and switched to a no-emission-filter spot on the dichroic turret, or where I was observing and for one reason or another (software reset?!?!) the excitation shutter opened inadvertently, I can say with certainty that if you work on scopes long enough, this WILL HAPPEN, and it’s not good.
Of interest is the FDA’s ophthalmic instrument guidance docs for retinal radiation (sec H 2.c). From my perspective, it’s surprisingly vague.
Because prolonged intense light exposure can damage the retina, the use of the device for ocular examination should not be unnecessarily prolonged, and the brightness setting should not exceed what is needed to provide clear visualization of the target structures. This device should be used with filters that eliminate UV radiation (< 400 nm) and, whenever possible, filters that eliminate short-wavelength blue light (<420 nm).
“The retinal exposure dose for a photochemical hazard is a product of the radiance and the exposure time. If the value of radiance were reduced in half, twice the time would be needed to reach the maximum exposure limit.
Bottom line, if you have a scope which is equipped with an emission filter wheel, this is something you should address.
If you have an extra Raspberry pi around and want to try something fun, you can use the GPIO on the pi to transmit at FM frequencies. For the rPi v1 you can use this link for instructions. For Raspberry Pi2 I found a great application which can be run from the command line, called PiFmRds . Not only will this broadcast audio from a number of sources, but it will also broadcast text, and can issue the station ID info! Really a neat experiment.
To use the Raspberry Pi 2 with PiFmRds follow these steps:
Configure an SD card with Raspbian or other linux distro.
Connect an antenna wire of appropriate length (or none for low range!) so as not to violate local laws
For the next work, we’ll use the Terminal.
To play any file format other than wav or ogg, install Sox
sudo apt-get install sox
Install the sndfile library using
sudo apt-get install libsndfile1-dev
Install pifmrds with the following 4 commands
git clone https://github.com/ChristopheJacquet/PiFmRds.git
cd PiFmRds/src
make clean
make
Now you are ready to run the program ***when in operation, if you click on anything outside the terminal it will freeze the rpi. I recommend stopping the play service using CNTL+C before attempting to even use the mouse!
for a list of commands on playing a file and setting a frequency, see the pifmrds page.
Here’s what you should see from PiFmRds, if everything works correctly:
Example output from PiFmRds
*Bear in mind that running this in a way so as to provide signal @ 200ft from your location can violate FCC regs! (see this FCC notice ). Obviously, for a number of reasons, I recommend you take extra care to comply with regs.
What do you think of the new site layout? I was looking for a simple, clean interface that works well on conventional and mobile browsers. Hopefully, I’ve found it. If anyone has recommendations, please feel free to comment!
One of the best aspects of flying is being apart from the world. Not only terra firma, but the troubles of life, questions of the future, and concerns of the present. Flight requires attention to instruments while in operation, but long cross country flights leave the pilot with time to sit and watch the world unfold beneath as time passes.
Departing from San Diego @ ASCB
Night flight brings an even more isolated perspective, where after a few minutes alone, you watch the gauges, view the small points of light from far off cities, and feel suspended in the air, utterly alone in the earth.
Night Flight home in the cessna.
So last night, flying home with the sun setting behind me, I had a chance to consider the past week of ASCB, and what it meant to me.
Trade shows are hard. They are hard for the attendees and the exhibitioners. Attendees sit through lengthy talks, then browse the show floor and get bombarded by marketing, then have dinners with colleagues into the night. Exhibitors aren’t that different. Business meetings in the early morning, standing at the show floor booth all day, and then meetings and dinners with colleagues and contacts into the night. By the last day, everyone is happy to rest on the trip home!
Yet somehow in this internet era, there’s nothing like meeting face to face, to share life, to discuss new projects, and meet new people. This year was my 14th year of attending trade shows as a member of the microscopy community. In that time things have changed in many ways, and are exactly the same in others. I hunted through the Blanco archives and found a few shots from my very first trade show. What an impression it made on me! This was from Neuroscience 2001, with my good friend Will Casavan. I was there working for Technical Instrument Company at the time, and Will was with Media Cybernetics.
Little did I know that it would be 14 years later, that Will would link me up with Echo labs, and a new and exciting chapter in my life would begin.
I bring up the past for two reasons. First, because I enjoy looking back to see how far this industry has come. 14 years ago the hottest product on the market was the Nikon TE-2000, and it sported 2, yes 2!, cameras. One for fluorescence, and one for brightfield. The inverted microscope with cameras, computer, capture cards (yes, the cameras required a card, check out that data cable!), monitor, supporting electronic boxes and cables, took up a large bench worth of space, and ran about $65,000.
Noelle looking at a TE-2000 microscope equipped with fluorescence and brightfield cameras
Some might argue that this industry hasn’t evolved quickly enough, but consider the following. Almost every function performed on the microscope above can also be performed using the ECHO Revolve. Of course, while at the booth I was able to airdrop images like this one straight to my phone, allowing me to easily post them on the blog!
Three channel fluorescence captured and airdropped to my iPhone in about 30 seconds using the Revolve microscope
To me, this is a major step forward in research technology. I think the attendees who visited the ECHO booth would agree, as while working the booth I don’t think there was a single minute without at least 1 person looking at the scopes. In 2 of the 3 days I worked the booth, we couldn’t even break for lunch!
Yes, I was there, yes this is a selfie, don’t judge me 🙂
While writing this, Eugene Cho, CEO of Echo labs, sent me a great timelapse of the show. I think this is an excellent video, as it shows the additional hard work required for exhibitors, to set up and tear down these displays. ECHO hand made the booth for the show, and the personal touch really made the booth stand out from the crowd in my opinion!
Of course, there are many other advances taking place in the industry! I got to speak with Silvia Foppiano of Oko Lab, and was amazed how far incubation technology has come! In 2001, the best incubators I remember were homemade ones. Today, you can buy a stage top incubator, with magnetized connectors, micro-scale thermistor temp probes, humidity and co2 control, for prices around 1/3 of units in the past. As a machining junkie, I was very impressed with the finish of these units. If you are looking for an incubation solution you should definitely check them out.
Magnetized hold downs keep the chambered slide in place when being used with immersion oil
This little controller provides control and capture of all sensor data in the system.
Chamber has perfusion ports for dynamic experiments
Zeiss has an awesome Oculus Rift-equipped demonstration of interactive sample observation. I couldn’t believe it when I walked by, there was the rift, and no-one was sitting in the demo chair! Boom 🙂 I had to jump on that chance. As a tech nerd and gaming junkie, I’ve been relishing the chance to test these, and it was a super cool experience! At first it’s disjointed to turn and see the image field move with the accelerometer inputs on the rift. Navigation was performed using an XBOX 360 controller.
Zeiss ad for the Oculus Rift Cellular Visualization demo
In only a few minutes I found my senses immersed in the environment, and was soon able to fly around with ease without even thinking about the control inputs required to do so. It really was like being in another environment. Excellent demonstration by Zeiss, and I’m happy to see that these types of technology are being adapted for use in biology.
Sutter Instrument Company had the new IPA Integrated Patch Amplifier system on display at the show. This system is a huge leap forward for cell physiologists. With a single system, you get a matched probe, amplifier, and digital capture device, all optimized for low noise and maximum sensitivity. Definitely a major step for whole cell analysis!
Sutters new IPA cell patch system
Open-Imaging had a booth as well, demonstrating the new Micro-Manager 2.0 open source microscopy platform.
I’ve seen a lot of new (read unstable) software at shows like this, and was surprised at how smoothly things worked. It’s obvious that Chris and Mark have put lots of time into this version, to make sure there’s minimal chaos factor when end users upgrade. I was also able to spend some time talking with Mark, as we flew to the show together this year! I’m excited for the future of Open Imaging, and am looking forward to working with the new release!
Mark Tsuchida takes the controls of a Mooney 201. We were speeding to the show at about 225MPH when I took this. Mark flew great!
I want to give a special thanks to Sutter and Open Imaging, who both allowed me to present my Triggerscope at the show. I hope you got a chance to see it!
My second observation is more a felt sense than a metric. Maybe it was the new product advancements, or my age, or who I spent tim with, but I felt a shift in generational control of the industry. During my early years in microscopy, there were a group of highly intelligent, capable and dedicated people who, in one form or another, directed the outcome of products and services in this industry. But now, a decade and a half has gone by, and I’ve realized that a new group of people are influencing that direction. While I may never get to place my personal mark on the industry, I know that I get to work near those who do. To the people who led us here, I’d say thanks for working so hard to bring this industry such incredible capability. To those who now have the burden of keeping things new, I say bear this responsibly, not lightly. Our industry should be the hallmark of the highest ethical standards, have the strictest dedication to accuracy, and consistency. Our marketing should keep people captivated while only promising what we can deliver. We should price products fairly, and support them well. I hope we are up to the challenge, because it’s in our shoulders now.
Yet…..when I did get a chance to walk the show floor this year, I took heart. I can see that the future is bright 🙂
Austin
Sunset after the show, from the top of the SD convention center
Ever notice that no matter what zoom setting you use on an iPhone, the resolution of the captured image is the same? This defies convention, as normally, as a sensor is cropped digitally, the resolution of the resulting image should decrease. With Apple iDevices, this isn’t the case. The native resolution is always the same, regardless of the zoom setting used!
Both of these images have the same XY resolution from the same iPhone 6s!
But some cropping MUST be going on, as there isn’t an optical zoom assembly inside the iPhone. At the same time, looking at the file sizes of captured images, it’s obvious some compression is employed, and one must assume this compression is near lossless for a given mag, so the Apple gurus must know what the true resolution of a field is, and employ a scaled compression to not exceed the inherent resolution of the captured image. Or rather, that’s what I assume is going on.
In order to test this theory, I printed an ISO standard test image (ISO 12233 @2014 to be specific), set up my iPhone 6s at a distance of 22″ from the target, and obtained a set of images, increasing in magnification from 1x, to the maximum allowed “zoom”, with as discrete steps as could be managed with touch controls. In total I captured 29 independent magnification steps.
First, here’s a look at the compression change over mag. For each image captured, I recorded the gross file size. Plotting this shows a direct inverse correlation between mag and filesize. As we know the resolution and bit depth of the file is unity, the only change must be the compression level used for a given mag setting.
So the next question is, how is maximum optical resolution (or rather “system resolution” affected by increases in magnification? The common method used to determine this for microscopy systems is the Rayleigh criterion , which basically says that maximum resolution is determined by the smallest spacing measured between two points (referred to as “minimum resolvable distance”). So in this case, we have a nice set of lines which gradually get closer together, and thinner, and which act as an excellent test standard we can use to compare maximum image resolutions.
Quick caveat here – my method of determining when minimum resolvable distance has been reached, is to use a dynamic ROI profiling tool on a line scan, and drag the line towards the thinner set of line spacings, until I cannot resolve in the ROI profile window, a measurable separation between the lines. While I admit this isn’t a hyper accurate method, I believe it to be adequate for this purpose. Anyone who might have a better solution is welcome to share!
So – here’s an example of a measurement on the lowest magnification. The steps to perform this measurement are:
Open sample image using Fiji
increase image zoom until horizontal resolution lines are clearly visible
Draw vertical line
open ROI profiling tool
Move line towards minimum resolution until no separation is visible between one line pair.
Move line back until pair lost is recaptured.
Record result.
So how does resolution compare to zoom? This graph is quite interesting! Note that a subsample of the total available images was filled, once maximum resolution was reached.
What’s compelling here is that the maximum resolution is reached at a relatively low mag value of ~ 1.496x. Further magnification beyond 1.496x would appear to only reduce field of view, and corresponding filesize. What’s also interesting is that the resolution available to the phone owner can INCREASE by using zoom! This is not normally the case for cameras which employ “digital zoom”.
How can you leverage this information? The next time you want to capture a distant scene with your iPhone, and want to capture the maximum resolution available while also snagging the greatest FOV, set the zoom to around 30% of the available range, and you’ll have a good balance between resolution and field of view!
*Notes
Zoom was calculated by comparing the size of a target object in each image relative to the lowest magnification image.
If you’d like to view the source data collected during this experiment, it’s available here. *Images are also available, please post a request if you’d like them!
I’m excited to announce 2 new products from Advanced Research Consulting. The first is a new, 16-Channel, 16-Bit DAC controller. This controller uses a high accuracy multi-line DAC IC to provide more DAC lines than any other product available for the microscopy market. A fully compatible micro-manager driver, as well as a text based programming library are included.
New TriggerScope16 Capabilities:
Set the controller up to perform pre-programmed functions, up to 10 functions per program, with a fast-switching array of 6 program blocks.
<1mS switch time for all lines
Optional setup for your devices, using either 0-5V, or 0-10V control ranges. These are configured at ARC, but can be changed at a later time should you need to work with new devices in the future!
Save-File function in micro-manager driver. It’s now possible to write a simple .CSV file, listing each program to run, and then load that file using a single command in micro-manager. This makes setup quick and reliable.
New custom extruded aluminum case
Optional connectors for your application. Purchase includes 2 D Sub connectors built to suit your needs, just let us know what hardware you wish to control!
Triggerscope2 is an update to the original triggerscope. I’ve that customers weren’t using the screen or the control knob in manual mode. Removing these has allowed for speed increase in all modes of operation, New output options allow for control over a wide range of devices, feel free to get in touch if you want to see if the triggerscope2 can work for you!
New TriggerScope2 Capabilities:
Basic configuration with 2 line TTL control
Custom Programming included with purchase!
Full micro-manager control included
Run sequenced programs, or run you own custom programs!
Expandable to include DAC, RS232, USB and multi-line TTL
New custom extruded aluminum case
You can read more on the triggerscope controllers on triggerscope.com.
In my previous post, I reviewed the current performance of available microscope control applications like Metamorph, NIS Elements, and Micro-Manager. Of course, using the Metamorph software device streaming function produced a hands-down winner, if you are looking for a simple commercial solution. On the other hand, many researchers are using the Micro-Manager software package, which is free, and quite fast considering it’s free. But what if you want an even greater speed, while using Micro-Manager? This is where stand-off controllers, like my device, the Triggerscope, or others, like National Instruments cards, or the Esio controller, may be considered.
Each option has it’s own advantages and disadvantages, but you really won’t go wrong with any of them. Deciding to work with triggering is a bit of an educational hurdle, but will allow you to become a far more powerful imaging jedi, as knowing how to make stuff work quickly can greatly expand the possibilities in your imaging!! So – even if you are considering one of the competing products available vs. the triggerscope, I say no matter which way you choose, a stand-off controller is superior in it’s inherent capability compared to PC based control. Why?
Reliable: PC based control requires drivers, drivers require a lot of development work, and they live inside the operating system’s environment, that environment is always changing (available RAM, processor time, etc) and is competing with other applications for resources. A stand-alone controller has a relatively static set of code in firmware, which basically either runs or won’t run at all. It’s a LOT more stable and reliable, not to mention that a windows OS update won’t blow it up!
Inherently Open: With voltages and TTL signals, you are free as the owner of such a device to basically drive anything you want. Filter wheels, lasers, piezo focusing modules, galvo mirrors, stepper motors, really anything you can imagine. This is not the case with software-specific device drivers.
Fast: While applications like Metamorph are quite fast, even meta sits underneath the stack of the operating system, and is therefore limited by the resources and access the OS will provide. microcontroller based solutions operate at the base level of the OS stack, or as low as you can get without using an FPGA. So these devices operate basically as quickly as it’s practically possible to operate.
Here’s a video I recorded recently demonstrating the speed potential for a stand-off controller.
Control Modes
Generally speaking, there are 2 ways one can use a stand alone controller with an existing microscope. For this example, let’s assume we are using a TTL controlled LED, and that we also have analog control over the intensity of the LED.
Master Control – In a master control mode, the controller will be used as the core clock for other devices in the system, thus the master will direct other devices to do things. In this example, the Triggerscope would run a program wherein any time latency or delays, would be pre-rpogrammed by the user. The user, or software in the computer, would tell the program to “ARM”. Operation sequence would look as follows:
Software sends “ARM” to controller
Controller runs program # 1 which is stored in memory
DAC’s, TTL’s are updated using saved stuff inside program 1
If a delay is added to program 1, a wait for the delay duration is executed
With program 1 complete, controller runs program 2, and basically repeats # 2 above.
Operations 2&3 are repeated until the maximum program # is run.
Controller reports that it’s done working to the host computer
Here’s a block diagram showing this configuration
Slave Control – In this configuration, the controller has a list of programs to run, but will wait to run each line based on the camera’s input. This can be useful when the camera may have a long timelapse due to exposure, or when the microscopy software may intermittently control the camera, based on other inputs. (for instance, maybe the software is driving an XY stage, and will expose the camera after stage movement is complete). Operation for such a setup would look like this:
Controller is sent an ARM command from software
Controller waits to run program 1
Camera sends TTL pulse or high to controller
Controller runs program 1
Controller updates DAC and TTL lines as specified in current program line, stored in memory.
If a wait value is specified, controller waits for the specified duration
When program is complete, controller returns to step 2, waiting for next program to run after trigger in.
Steps 2-4 repeat until last program specified has been run.
Here’s a block diagram of this configuration:
So how fast can a system like this run? Here’s a screen capture from a recent oscilloscope run. This was using my generation 2 triggerscope PCB. In this example, there’s about 1.4ms of total system latency, meaning that a maximum speed of 1000/1.4 = 714fps is theoretically possible. In the screen capture below, the yellow line is a DAC line, the blue line is a second DAC line, and the magenta line is a TTL line.
Let’s investigate this a bit further. In the above sequence, the Triggerscope was configured for master mode, with 10ms delays per line. the 2 DAC’s were updated and the TTL was controlled during the operation of a total of 4 program lines. If we look a bit closer at this graph, we can measure the width of these signal changes:
Note here the BX-AX measure of 11.3ms. This should be 10,0ms, so we have 1.3ms of latency
For each step in the program list, we can measure ~ 11.3 or 11.4ms of total delay. Why is this 1.4ms of delay present? It turns out that in this particular IC used for DAC, the communication method used, and the response time, adds up to ~ 1.4ms. This can be seen by viewing a comparison of the DAC line change vs. the faster, and direct, TTL line change:
In this example we can see a 0.5ms, or 500uS, delay in the TTL signal
For the above example, we can see a measurement of 500uS. This delay is the delay time of the TTL line, over our specified 10ms wait on the program. What this shows is that the controller can operate at ~ 2000FPS, but this particular DAC requires an additional 1ms to operate.
Conclusions
Standoff control systems like the Triggerscope require a bit home homework to set up, but I hope the examples above prove the benefit of such systems. Very high speeds can be achieved, or rather, speeds far faster than most cameras can capture light at! Additionally, the open nature of these systems allows end users to set them up for a wide variety of uses, from light, to fluid delivery. Best of all, these controllers are essentially “crash-proof”, eliminating the commonly experienced random crashes found with typical microscope control software.
I’ve been working with Arduino boards a lot lately, and they are great. But some elements of the arduino can be even better.
What is an Arduino?
An Arduino is a breakout board for the Atmel “ATMega” series of microcontrollers. These microcontrollers allow for high speed measurement of analog and digital signals, as well as high speed output of analog and digital signals (well, quasi-analog using PWM, which is another post). So, the arduino houses one of the ATMega Chips at heart, and provides things like a voltage regulator, Serial – USB adapter, 1mm pin connections for several of the chip’s pins, and other nice to have or required-for-operation items one might want or need for these chips.
Now, there are large Arduino boards with a great number of pin connections, like the Mega2560. This board has a ton of capability,
Arduino Mega2560 pinout Diagram from Pighixxx
with a great array of connection options. On the other hand, there are super small but capable boards like the RedBearLabs Blend Micro – which includes BOTH an ATMega ship and a BLE transciever!
But each of these options has drawbacks, cost being one. The Mega is around $45, and the nano or tiny boards even without BLE are ~ $11. Yes, this is cheap, amazingly cheap considering the capability they provide, but if you want to integrate these into several projects, this cost aggregates rather quickly. So, can we go cheaper? In many cases, the answer is yes, and it can be found in the excellent little ATTINy series of controllers.
ATTiny pinout
The ATtiny85 is excellent for sensing a few lines on input, and driving a few outputs, like an LED, or speaker. For powering the IC, I prefer using a USB cable, which usually provides a clean source of 5V power.
Now, to program the IC, you’ll need a programmer. The folks at Arduino have conveniently included an option for “Arduino as ISP”. Basically, you use the communication lines on an existing arduino to program your Attiny. I’ve found that a homemade shield makes this easy, as when you need to program an IC, you take any arduino laying around, drop the shield + chip on, program, and then continue using the arduino board for whatever project you’ve got. An example of a shield for an Arduino mega can be seen below. It took maybe 15 minutes to get this wired up – not a pretty solution, but fast and easy to use.
Of course, you don’t need a shield to program the IC’s, a breadboard and some jumper wires will do.
Once you have the IC programmed, it’s a matter of popping it out of the socket (or breadboard), and placing it into whatever socket you use for your project!
There are numerous examples online of how to program these chips, a few of which I’ve used as guides. I like the one here, and there’s a nice video showing the general process here:
Anyway – if you do plan to tackle this, just make sure to follow the directions for your specific version of Arduino IDE – there’s a big difference between v1.6 and the earlier version(s). ***IMHO, V1.6 is WAY easier to set up.
Every so often I will get the chance to cook up some code for one of the usual software scope control packages. But these days, I spend most of my time in programs like Fusion360, Fritzing, and the like. So I guess this is how I feel when using the typical scope control software. How about you?
I’ve used Elements, imagePro, MetaMorph, for years. It’s all good software. It’s powerful, and can do all sorts of crazy things that are super awesome. But what if I just want to obtain a 3 channel fluorescent image? Here’s what I end up looking at for a simple capture.
Screenshot from NIS Elements – Lots of options, but lots of buttons!
But this must be only one program, right? Surely other more capable systems have a current style of user interface, right? Here’s an example of the most capable (and IMHO fastest) software around, the venerable MetaMorph.
Another example of great software, Metamorph, that includes a large array of buttons….
For the typical person who just wants to snap an image, this is overkill. Now – I don’t intend to bash on these great software applications. For multi-dimensional timelapse, or other advanced work, there are few better tools available, and these do a great job of providing any feature one could want. But what percentage of labs have such complicated instruments, vs. the great number of simple, multichannel fluorescent microscopes around in every biology facility? How can it be that all these users must learn these behemoth software packages to capture some cultures? Other industries seem to have moved to workflow-based designs. You can find apps that perform full MIDI mixing on a tablet, heck, even airplanes have touchscreen controls now! Yet the microscopy industry seems to be locked into a slightly improved version of windows XP button mashup.
With all of the consumer products finding ways of simplifying control over hardware, isn’t there another way of doing this?
Good software design can perform a specified job, and provide users the controls they need to do that job, but excellent software does so without requiringany training. An example of this can be found below, showing a unified interface for shuttering, attenuation and capture. This is a very limited example of what’s coming up, but just from this clip I think the differences in design philosophy are evident.
Can this simple control drive shuttering, attenuation and capture?
I think Scotty wasn’t annoyed at the keyboard because he had to use it. He was annoyed because of what it represented: A barrier to getting his work done. Microscope time isn’t free time. There’s a lot of other, far more important work to be done than collecting the results of actual research. Cumbersome software results in less time to do the important stuff.
Complex software will always be required for highly complex jobs, but for everyone else, I’m happy to say that the days of “software training” will soon be behind us. My guess is that most people will have a hard time going back to click and hunt, after using the next generation of control software. I know my perspective has changed. I guess that’s why these days, when I sit down behind a button-crowded screen, all I can think of is Scotty cracking his fingers 🙂
I came across this excellent design reference, which shows quite a few basic op amp design examples. Great guide to keep handy should you be working on amps!
Does your system crash when taking a timelapse, or just every so often, but isn’t linked to a specific set of actions you take? Or, does your camera run slowly for no apparent reason, only sometimes? Here’s a basic set of checks to do before targeting the software drivers or hardware.
Windows power options
So windows by default wants to save power. It does this by turning off stuff when those items aren’t “used”. But for research systems, we want these devices always running, even if they aren’t feeding data at the time.
Open Control Panel in Windows (Make sure you have administrator rights to do this)
Open “Power Options”
Make sure “High Performance” is the active plan.
Click “Change Advanced Power Settings”
Browse through each item and make sure things like “USB Selective Suspend” is Disabled. My system looks like this:
Turn Off Hard Disk : NEVER
Wireless Power Saving: Disabled
Sleep Settings : Disable everything
USB Selective Suspend: DISABLED *this one is important!
PCI Express Link State Power Management: EVERYTHING OFF
With these changes made (if needed) click APPLY then OK.
USB Happiness
USB bandwidth is divided when several items share the same USB hub – so for instance you might get a hard drive on USB running nice and fast all by itself, but as you add more stuff to the USB hub it’s running on, it’ll run more and more slowly. In order to avoid this on our systems we need to manage what devices are sharing ports.
Next we’ll see whats going on with USB devices. For this, we need a program called “USBDeview” found here.
Install + run this program. You’ll see a tree of your USB devices. To make sure only connected and active devices are displayed, click View, and turn off “Display Disconnected Devices”. What remains should be those devices connected to your computer. My computer only shows a tablet pad right now, but for a typical imaging system, there will be many more items!
Slide the view bar to the right, until you see the column for “HUB/PORT”. This shows what USB hub and port your hardware is connected to. So, if your camera is connected to HUB 1, and a bunch of other devices are also on HUB 1, then this can cause the bandwidth of your camera to be drastically reduced!
Note this is sort of a “musical chairs” game, where you’ve got to figure out which devices you want to have the most bandwidth, and sort them into hubs as desired. As a general rule, devices fall into 3 classes:
Cameras – most data, should have a hub all to itself if possible
High speed UART devices (those scopes and devices NOT using a standard COM #)
Serial Emulated Devices running at 9600 Baud – these are easy in terms of bandwidth and don’t need a lot to be happy.
Mice/KB/other user hardware – this stuff isn’t critical, so should be relegated to a “don’t care” hub.
With these changes, try out your system and see if things work better. More to come on this subject!
I’ve had an actual “job” since I was 15. Of course, my first work was mowing lawns as a kid, moving firewood, cleaning up rental houses, the usual “make a few bucks” stuff. When I was 15 I had a chance to become a beta tester for a book called something like “Windows 3.1 for kids”. Of course, once that book published, I had to enter the real workforce, which led to the upper crust position of Jack in the Box grill guy. Over time I moved up the ladder to Wal-Mart, pushing carts, and ultimately working in the electronics department. In my junior year of high school, I joined a small independent computer shop in a strip mall called ICB computers, managing to get in 40 hours a week while in school. There I beat my head against the wall trying to resolve IRQ conflicts by swapping jumpers in ISA cards, installing the oh-so futuristic 5″ “bigfoot” hard drives, and generally figuring out the world of the PC. Many years and jobs later, I’m 35, so I’ve had a full time job for around 18 years.
It was this comfort of always “having a job” which caused me to struggle with a very tough question – was this the time to branch out into my own business? Would there be enough work for me to sustain my family? Could I manage such a daunting task? Ultimately, I was compelled to take the step, and as of Oct 2014 have launched Advanced Research Consulting Corporation.
[EDIT]
Originally I planned to stop blogging, but I’ve had a number of requests to keep it up! So – I must bow to the community and get back to frequent posting. 🙂
I’m happy to announce a new product for microscopy, the “TriggerScope” controller system. I hope this device will prove itself useful in many areas of microscopy, but the basic idea is that it can drive scope components via manual control, TTL triggering, or PC control.
Let’s say you have a laser and want to drive it, but want to use Micro-Manager, and there isn’t a straightforward driver solution – with this device, you can run the laser right from the triggerscope, control the firing sequence of the laser based on a camera, manual, timed or software input, or just control the laser manually. A block diagram of such a setup would look like this:
Here’s an example of a ramp setup showing on/off of 2 triggers (say 2 lasers) and stepping of the DAC output (in this example we could send the DAC to a focus motor)
The Controller can also be used as a straight controlled DAC system, where your PC drives the box and the box sends out TTL and/or Voltage values out. More information can be found on the website for the device.
The device shown is the base system – I can build these with up to 9 DAC outputs, and 20 TTL outputs. Custom software is also available should you want to do something unique with this. Also – the firmware and software code is provided with the device, so you can add to it if you like! As far as I know, this is the first device to be provided with open source firmware & drivers.
I’ve been experimenting with a simple way of pulling a single power source into two rails, ad the simple solution is to use a voltage divider. One of the best explanations I’ve found on how these work is this excellent tutorial from SparkFun .
I recently was working on some file transfers using filezilla, when I needed to edit a php file. Filezilla has a “view/edit” option, so I clicked it figuring, “ah, this likely won’t work, but I’ll give it a try”. To my surprize, it launched a really nice text editor, which after some research turns out to be Adobe’s Brackets. I tried this tool on Elements .mac files and on arduino .ino files, and while it reads mac files, amking external edits simple and clean, it properly color codes arduino .ino files, which is really nice.
Microscope objectives are typically classified as being brighter or darker based on NA, or Numerical Aperture. This is for good reason, as the NA of a lens will affect both the amount of light delivered to a specimen (excitation) and the amount of light collected from a specimen (emission). In addition to this, NA increases in both the X and Y axes, so a 0.1NA increase increases the efficiency of an objective by 0.1², which translates into a LOT more light. But how does magnification affect the brightness of a lens?
Consider a typical set of high magnification oil immersion lenses, let’s look at a 100x 1.4NA, and a 60x 1.4NA. If the NA is the same, we can determine that:
the minimum resolvable distance is the same (affected by NA)
the excitation.emission efficiency is the same (affected by NA)
So how will the magnification affect the overall brightness? If the NA of the lens specifies the accuracy we can resolve at the specimen plane, then the magnification of the objective relays that resolvable distance, to either a detector (camera) or our eye. If the magnification is low, the amount of information, or light, per unit area, will be greater, at a lower magnification. Kurt Thorne has a good example of this on his post regarding space bandwidth product, which shows just how much more information is packed into a 60x lens due to the larger FOV. So – if we have the same light collecting ability at 60x, as we have at 100x, then we have concentrated the same amount of light onto a smaller point at our camera, or at our eye.
What this leads to is that we have a choice of which resolution we want to maximize, if we want to obtain the most dynamic range, or the fastest capture frequency, or a large field of view, (or any combination thereof) we would choose the 60x lens. The 60x grabs a larger field of view, and packs the most light into the image sent to our oculars or camera.
On the other hand, if we want the absolute highest spatial resolution, say for a large-pixel EMCCD, then we could choose the 100x, to spread our light over a greater # of pixels.
It’s not uncommon for microscopes to be equipped with only one high magnification oil immersion lens, and usually it’ll be either the 60x or the 100x. So, if you are considering which lens to buy, or to standardize on for your research, consider the importance of both magnification AND field of view/brightness. You may find that a lower mag objective improves the quality of your data!
A friend sent me an awesome and interesting article on petapixel with some excellent examples of how rolling shutters work on cmos cameras. (Thanks Hoy!) This is directly applicable to scientific CMOS cameras, IF you are using the “rolling shutter” method of capture. To make sure you capture an entire field of view in one single snap, use “global shutter” mode.
But I’d add that the best place to find such tools is Harbor Freight. Now don’t get me wrong, I’ve found items like cutting tools, abrasive pads and the like to be of marginal quality, but for a lot of tools, you can’t beat good old HF!
Years ago I worked for a major imaging camera supplier. During one meeting with a team of engineers, we were discussing some really cool aspects of a camera and driver suite for that camera. The engineers were showing us “kinetic accumulation” modes of capturing pictures, sort of an “HDR on chip” technique. My question to the engineering team was this, “This is awesome, but I can’t do this in any of the standard image acquisition programs on the market like MetaMorph!” The response from the engineers was quite interesting. They said,“Maybe you can’t use this feature in MetaMorph, but you can easily do this with our proprietary software suite!”
This was the day that I realized how fundamentally disconnected internal development teams could be from a customer group. At a base level, any feature which isn’t accessible via the common software in use today, is a nonexistent and useless feature as far as the market is concerned. Who cares if any hardware device is chock full of features I can’t really use?!?! The world of imaging systems is more than a decade behind current user market understanding. Back in the early 2000’s, we’d put up with crazy email sync problems, calendars that just failed, drivers that didn’t load, and a host of other user experiences that limited or prevented the use of technology. But now, in many ways through the innovations of a few leaders like Apple, Tesla and others, customers expect to have access to powerful technology, while being able to use that technology easily. We want a “good picture” button for our imaging.
You are buying more than a widget for today
This leads us to an interesting aspect of the hardware and software components which constitute an “imaging microscope”. At a base level, all systems are just a collection of control software, communication/amplification control systems, and motorization or sensing devices. But to the user, the experience has nothing to do with the hardware! What the user feels, is how the software feels. This is a key point. Recently, I leased a Ford C-Max hybrid. I was impressed with the mileage and integration of the EV system, and wanted to lower my fuel bills. What I didn’t expect, and what really impressed me, was the level of control I was provided over the entire system – with the C-Max I could set the system to EV only, gas only, or “best use”, based on what I wanted for the day. Yet, if the system needed more energy than the EV side could produce, it’d auto-switch to gas supplement. When plugging in the car, you could easily determine how much EV power was available just by looking at the illuminated charging port ring – an LED circle indicated the % of charge – 1/2 circle meant ~ 50% charge available. A small feature, but one I’ve found I use every day. In short, I could easily handle powerful and complex technology, through simple understanding and controls.
In a similar way, the “user experience” of a system is truly found when you click and drag and change things in an imaging software package. What goes on under the hood to make things happen as a result of your click constitutes huge investments of hardware, firmware, mechanical and electrical engineering, but for a typical research experiment, I just want the thing to run correctly, use my settings, not crash, and provide simple adjustments to capture and control parameters.
How Components Control your Fate
So how do you take these complex truths into account when looking at buying, building or modding a system?
Consider that what you will feel most at the end of the day is not one component’s blazing speed, but the software’s ability to control that part of the system. So – check that any critical performance point, say, shuttering times, is not only supported in hardware, but that the hardware will run that fast in your software package.
Ask yourself what you plan to do with the system in the long run – do you see yourself always working with software brand X? If not, will the devices you buy today be compatible with other brands of software? Find out BEFORE you buy!
Check out how accepted your hardware components are in the market. How can you discover this? By checking out how many software packages support a given brand of hardware. As an example, any decent software package will support Sutter filter wheels – why? They have been around since the dawn of time, they almost never die (I’ve seen wheel setups still running that are over 15 years old!) and they are easily driven. In a certain sense, how many software packages run a given device is a way to measure how accepted that device is.
The above holds true for devices which are on the market for a few years, but what about brand new, super cool stuff? There can’t be wide acceptance of those components, as they aren’t that old! In this case, it’s a great opportunity for the new device manufacturer to show the product in a demonstration, using the software you plan to use on your instrument. Is there no support for your chosen software yet? You have several choices: Annoy the software manufacturer to write a driver, annoy the hardware company to write a driver for the software package, or contract a person like myself to cobble together a custom driver for you.
If the above 4 points are important, this is equal to their sum: Whoever you are buying your system from, whether a series of direct manufacturers, a dealership, or a microscope manufacturer sales rep, should be willing and able to do the above work for you, before you buy your system. This is the sales rep’s job – to prove his or her worth in helping you find the best configuration of parts and software for your work! If the rep isn’t willing to do this, then there’s not enough of a commitment to your success, and you shouldn’t reward apathy with a commission check. Good reps should be happy to show off what they know, and how great their systems are.
So there you have it – now you know that building a system isn’t easy, but that with proper homework, you can have a solution that will meet your needs today, and tomorrow, saving your lab huge amounts of headache and heartache down the road.
Some beautiful pictures of Saturn here. As a child my great uncle Dan, who worked on the fuel mixture system for the STS series shuttle, showed me saturn through a small telescope. I will never forget looking at those rings, and my wonder at how such a device could present such an image, funny how much this inspired my journey into the world of optics. Much More here.
When working with amplifiers, it’s crucial to keep as much noise out of your power supply as possible. Most of the time, your power noise will end up being amplified or will at least show up in your resulting signal as pattern background noise. To make things harder still, many signals are 0V based, and the source signal will swing from a negative voltage to a positive voltage as it is read out (AC). This is usually preferred as it produces a more stable output signal for a variety of devices. So where can one find a suitable power supply, which feeds both a +V and -V signal? This can be tricky, and high quality (read: cleanly power) units can cost a lot of money. But, for many applications, perfection is the enemy of good enough, and you can get away using a good – (but not perfect) power supply that can be had almost everywhere – via USB. Now any EE purist will shout “USB is NOT a power supply!” and this is largely true – USB was never intended to be used purely as a power supply. Then again, the internet was never intended to be a social media platform…
So – By snagging the +5V from a usb line, we can create a -5V using a simple IC, like this one from Linear Technology (LTC660). This IC is a simple 100mA voltage converter, which inverts whatever supply voltage is provided to it. A simple circuit for testing can be modeled in LT Spice, as I’ve done with one here:
This design follows the recommended one from Linear Tech, and is quite simple. What you end up with is a straight inversion of your source voltage, so providing this +5 returns -5 on Vout, or providing +3 returns -3 on Vout etc. (ignore the sets of decoupling caps at the bottom of the image)
The next question is, how clean is this design and using USB in general? I tried a few tests today, using a pc-based oscilloscope, and found USB to be nearly indescernable from the use of a super-clean voltage supply from a 9V battery. Here are some examples:
Below is a time average of both the positive and negative rails as supplied from a typical PC USB connection. Note the ~300mV + and – spikes on the source line.
Next is an Apple iPhone USB wall charger. A little bit cleaner than the PC based power supply. Apparently Apple makes a clean supply, as it dropped to 0.109mV of noise, or ~ 2% noise/nonlinearity. Note that I’ve also added a 0.68uF decoupling cap to the input +5v line in this test – the PC line shoed a reduction with this cap, but had about 0.070mV more noise than the apple supply did.
Here’s a fast time capture of the Apple wall charger, again with the 0.68uF cap included from + to GND before the inverter.
As a comparison, here’s a 9V battery. Overall a clean signal, but still some noise present. It’s entirely possible (probable) that this noise is actually in the scope itself vs. the battery. Note here (I know it’s hard to see) but the spikes on this # are about 0.20mV, which is about the same as the Apple USB charger! (the red line is the disconnected -5v rail – I wanted a clean test so this test was simply the positive side probe directly hooked up to the battery)
So what does this mean for the average tinkerer? I think using either a PC based USB line, or a nice high quality USB wall charger, as a simple power supply, should be considered as suitable for non-demanding applications. Of course, this is not as good as a high end power supply, but then again, I was able to assemble this circuit on a breadboard in 25 minutes, and it took a whopping $15 worth of components. So from a price/performance perspective, this can’t be beat!
I was talking with a long time friend from the MetaMorph team and was surprised to learn they have had an app-based control package available! I haven’t tried it yet, but the next time I get my hands on a meta-controlled rig I’m definitely gonna play with this. I think this would be great for group presentations, collaborative research projects or just being able to walk away from the scope without constantly wondering if an experiment failed to complete. Cool stuff!
This is a great explanation of why most news regarding evil dangerous “chemicals” or miracle substances are half-baked. I wish they’d play this as a PSA on evening broadcast TV instead of the usual stuff…
A great example of the whole correlation != causation is the pirate vs. global warming graph 🙂
This monday I had a chance to take a few shots of the moon as we caused an eclipse. You can see a bit of the “blood moon” effect as well. The shooting conditions were OK, high altitude stratus obscured the view, but it was viewable! My photography setup was on a small telescope and the camera’s shutter slap + weight + lunar movement caused some blur.
Note the artifact on the upper right – this is due to poor alignment of the camera and achromatic aberration of the scope.
Nikon D80 on ETX Telescope
The beginning of the eclipse cut off a portion of the moon but didn’t change the color.
Nikon D80 on ETX scope
Here I used an iPhone 5S placed over the scope’s ocular:
Once the eclipse took effect over roughly 2/3 of the moon the blood moon effect began to show. It was hard to capture, as a dim red glow.
Some longer explosures caused blur, but captured the blood effect:
Believe it or not, the larger shot was using the iPhone 5S on the scope. I learned a few things, chiefly that I need a better coupling system for my telescope if I expect to use this for any quality work, but it was a fun experience and a weird, eerie thing to watch!
For those on the west coast USA, this will begin just before 10PM, and conditions should be perfect (clear skies, dark, early enough to watch and not miss sleep!) – I’ll take pics and post what I get!
A new website observes that today’s scientific research is hindered by excessive regulation and oversight. On a spectrum of two possibilities, total anarchy in research vs. total control, where do we stand? I’d guess it depends on what part of science you work in, and where you work and live…
Ever since using services like AirBnB and Uber, I’ve been thinking of a system which would provide ride shares for pilots. Almost every certified airplane has 4 seats, but most flights are single pilot operations. Meanwhile, there are always people who need to get somewhere fast, or who simply would enjoy to fly. Why not marry the availability and the need? It seems that Steve Lewis and Andy Finke have done so, by launching airpooler.com. I’m hoping it’ll (ahem) take off….
Example Low Pass using only one resistor and one capacitor
I’ve been working on a project where I needed a consistent DAC signal to be sent from a control device to a sensor. The sensor wanted a voltage input which was steady, but arduino boards don’t have true DAC output, rather they use PWM to approximate a voltage over a given time. For many devices (like a simple LED) this is fine, but for higher speed systems, more precision is required. A simple solution is to employ a low pass filter, similar to that described here.
The site mentioned above has an excellent link for calculating your R and C values, based on the input signal your dealing with, which can be found here.
The Arduino IDE for ARM microcontrollers is just plain awesome. I’ve been using both an Uno and a Mega board for quite a while now, and continue to be impressed with how flexible these inexpensive boards are. Recently, I wanted to read the output of a pair of rotary encoders, like these: Encoders can be used for all sorts of things, from acting as a user control knob (with endless turns), to acting as a verification system for motors, to confirm that a commanded # of motor moves has been completed accurately. In fact, linear and rotary encoders are used on microscope stages for this exact reason, to confirm that the stage actually went some specified distance.
So – I wanted to use an encoder as a knob for user input. Encoders output a set of signals, which run either open or closed against a ground, based on the position and direction of the knob turn. An example of this can be seen below.
Now, the problem with reading an encoder is that usually, your microcontroller is busy off doing something else (executing code) when the user begins turning the knob. So, how can you make sure and check the input lines from the encoder, quickly enough so as to not miss a rise or fall? Keep in mind, if a fall or rise IS missed, you lose both the position of the encoder, but also can incorrectly interpret the direction of the turn. There is a handy way to accomplish this, by using interrupts.
Interrupts are what they sound like – if the code is running on the microcontroller, and an event occurs which qualifies as an interrupt-driven event (you can specify these, for instance, “interrupt if my input signal goes from low to high) then whatever is currently going on will pause, and the interrupt code will be executed. This relieves the author (to some degree) of having to maintain super tight code timing, which is great, as in many cases it’s useful to have a long operation or series of operations doing things on your microcontroller.
In my case I wanted to add the capability of dynamically limiting the encoder’s range, i.e. for some portions of my work, I’d want the encoder to have +/-100 counts of range. In another portion, I’d want the encoder to have +/-50 counts of range. In order to accomplish this I wrote a simple argument at the end of my loop() code, which read something like this:
byte range = 50;
if ( positionLeft > range){ knobLeft.write(range); }
if ( positionLeft < -range){ knobLeft.write(-range); }
in this example, if either limit is exceeded, the knob value is simply written to hold the last position, and never go higher than that position. This code has worked well for my projects, hopefully it’ll help you out also!
Just a heads up if you plan on using the NK Remote tethering solution for Micro-Manager. It appears as of now this solution only works in 32 bit installations of windows. I believe a great alternative would be to figure out a driver connection to the open source program DigiCamControl…but as I’m not that great at writing drivers….
I was just thinking about this issue on my morning walk. So my wife and I travel to Mendocino, and there’s no cell coverage. On one hand, it’s kind of nice to be disconnected, but on the other hand, I’m thinking, if some entrepreneurial person could figure out the hardware/software setup, they could make a killing hooking up a cell transceiver to an internet connection from home….cool stuff!
This is an interesting proposal to deal with the “watchers causing a change” phenomenon in quantum mechanics. Of course, answering this would answer the question of “free will”. Crazy!
There’s a funny, and interesting youtube video on this called “Dr. Quantum”.
I think this type of hyper-focal imaging tech will bring as yet unimagined possibilities into photography. Remember when the idea of a Digital SLR was ridiculous, because CCD’s didn’t have the dynamic range or resolution to compete with film? Next, consider how over time, each problem was addressed in a novel way: High Dynamic Range images not only solved the well depth problem, but brought a new wave of photographic style. Resolution was improved as the technology matured, but stitching of images addressed the resolution problem in a different way.
So, is this technology going to render the “single sensor” camera obsolete? Only time will tell, but there are some VERY novel things one can do with a camera system like this….
I remember many years back when I was 10 years old, I had a friend at my house, along with some family. I was proudly showing off piles of electronic parts which I had scavenged by disassembling anything I could get my hands on, and one of my family members mentioned, “Oh yeah, that’s more of Austin’s junk…”.
Fast forward 25 years, and what I learned from obtaining that “junk”, is what feeds my family. The lessons I learned as a child, the lessons my parents gave me the opportunity to learn, built a foundation of understanding which I leverage on an almost daily basis. What if my parents had not let me take things apart, as that would have been far too dangerous or messy, right? All those sharp edges and electrical wires? What if they hadn’t allowed me to build, and later race, remote controlled airplanes? The skills and lessons learned in my projects, servo control, radio control, engines, wing design, weight and balance, epoxy and fiberglass work, wiring, soldering, power, have popped up again and again in today’s work, and have allowed further pursuit of more serious work.
I recently completed an optics class at my oldest son’s school. In teaching this class I learned two things, one, It’s hard to keep young adults focused! Secondly, and of far more importance, is that they are able to learn, and do, far more than we give them credit for. Most people consider 18 simply too young to be responsible, and yet at 18 we have members of our military driving tanks, submarines, patching up wounded soldiers, or making a decision whether or not to shoot another human being under the fog of war. We expect far to little of our younger generation, and they rise to meet our expectations…
Of course, no one doubts that the thinking of a person with years of failures behind them is far more pragmatic, but we allow far more mediocrity in our youth than we should. We expect far less than they can do, and is it then any wonder why they are bored? I remember hearing as a child a simple phrase, “If you shoot for the bottom, you’ll hit it every time.” By basing every test we place for kids on “what if the last kid feels bad?”, we devalue the effort and ability of those who excel, we rob the winner of deserved merit. As a parent I’m making every attempt to involve my kids with my work, the good and bad aspects of it, the technology I use, and my passions outside of my career. I’ve found more often than not they grasp concepts which I’d never imagine they could understand. Why not push a little harder to see what they can do and grasp, and allow the opportunity for learning to take place in failure? In every endeavor I’ve taken on, I’ve found that I am educated in defeat and failure, and learn only to increase my ego in success.
For those of us who are parents, why not place that little bit more extra effort into involving the family in your work and projects? For those of us who aren’t, why not lend some of your time to a local school, church, or community organization where you can share what you’ve learned to the next generation? It’s up to us to enable youth, and if we fail to do so, it’ll affect our quality of life in the end! Who knows, maybe you’ll inspire the next breakthrough idea in the mind of a child, simply because you shared a small chunk of your time and knowledge, or set a high standard, only to allow them to realize their potential in achieving that standard. The next generation can be as bad, or as great, as we encourage them to be…
About a year ago I backed a Kickstarter project for a 3-D printer. A few months after some typical Kickstarter delays (production trouble – etc), I received my shiny new printer in a big box. After setting it up I realized one thing: I had no education in this method of fabrication – and I was about to invest the inevitable amount of time suffering (learning through failure) that any such new field requires of the neophyte. In addition, I was reminded that advertising is just that – advertising. The sales pitch of 3-D printing is at it’s base level this: “Anyone can make a part, and have that part fabricated at home or at the office, using a 3-D printer.” Of course, like all sales pitches, this is true with several qualifiers! I’ve only begun what I know will be a months long or years long journey into learning this technology, but I thought I’d list a few observations for anyone considering stepping into this world:
Halfway through a print…
You can’t make what you can’t design.
Printing parts is one thing – designing parts is another. Fundamentally, I’m not a mechanical engineer, but to make a proper part, I need to have some experience in mechanical engineering, i.e. will the thickness of a part based on it’s material sustain the forces to which it will be subjected? How about when it’s 110 degrees F outside? How about vibration? Will the part warp? What is the tolerance for usage? For manufacturing? Now, some of these questions are easily addressed – when in doubt overdo it. Use 2x thicker construction, use aluminum when plastic would suffice. For research work, this is acceptable practice, as only one part usually needs to be made, and typically the part only has to last for a series of tests. Now designing a part to be mass produced? That’s a whole nuther animal. So before getting super excited to print stuff, one must ask, can I make what I’ll print? And that leads me to CAD software.
CAD is King
Before you print, you’ll need to obtain a part file. This can be done using a variety of programs, but I have come to enjoy the open source OpenSCAD program. The software is cross platform, parts can be designed using parametric relationships, and is basically a “code written” part design tool. I.e. you call out an object and it’s properties (a cube would have XYZ dimensions for instance) and as you add, modify and intersect parts you can form more and more complex shapes. Others use programs like solidworks, which is from my understanding one of the best programs available for the in depth engineer, or autocad. With both programs the barrier to entry is high as each costs quite a bit to purchase a license. My work is simple, so I don’t need super awesome rendering tools, and I was looking for something which I could quickly learn, which led me to openSCAD, and I’ve been very happy with it.
This is a Gear I designed using OpenSCAD and a plugin.
CAM Processing, or Slicing
Once you have a design, you’ll need a tool to figure out how to lay down filament in order to build that design – this is where things can get quite technical. For instance, I kept having failed prints, because my filament would stop feeding halfway through a large print run (5 hour for example). I found after much experimentation that the error was caused by a lengthy filament retraction – on- move command inside of my CAM program. Addressing this has resolved the issue, but this is where quality, reliability and success can be greatly impacted. I use a program called Slic3r, which has IMHO some of the best documentation I’ve ever seen for explaining various buttons and knobs in any software package. Slic3r and other CAM packages generate toolpath commands, referred to as GCode languace or sometimes NC (numeric control) language. This language is somewhat verbose, so you can write or edit it – i.e. G01 x100 would send the machine to x position 100. Relatively simple. Different CAM programs will provide various levels of user control of all sorts of things, so you can go as easy or as controlled as you like for your personal taste.
GCODE Control
Once you have a gcode set, or rather a toolpath, you’ll need to control your printer and feed the toolpath commands to it. Several freeware open source applications exist for this, of which I use Repetier. Repetier software is great as it has a CAM processor built in, so I can go from a model file, to sliced gcode commands, to machine control, all in one program. 3D printing is really a great example of a field where high quality professional software is available for free – but if you do use it please find a way to support the community – either by buying products (like filament) from companies who fund these programs, or by adding to the program or community yourself.
Results
Aren’t easy at first – I had issues with prints not sticking to the print bed, filament jams, delamination, warping – each problem was an investment of hours, coffee and brain time to figure out – along the way I’ve learned a lot about how much I don’t know about 3-D printing, but it’s been a very worthwhile education. Now what can one do with such a device? Well in my case I’ve long wanted to CNC convert my mill, so I’ve designed some gears in OpenSCAD, and printed them, and attached them to my mill…..
This is an interesting way to use image processing. It’s a program which encodes text into an image or into a sound file. Looks like something for the spy world but it’s something I never considered for image processing. Cool stuff!
So over the past year I’ve been working on a product which I can finally talk about. It’s a retinal imager which uses the iPhone 5/5S as a capture/storage system. For now the only specs I can give is that the images are wide field, and that it’s intended for patients who are dilated. It’s been quite a labor but I’m really happy with the results. The short form website for the device is here.
Below are some pics of the finished prototype units. What’s been really cool has been the rapid prototyping of these devices. It’s amazing what can be done with modern SLA machines! The tan pics show my 3rd gen iteration, where the black/white units are the 4th gen. This is intended to be a low cost system, while producing high quality images similar to what is obtained from currently available fundus cameras.
I’ve had a chance to play with an Arduino Uno for the last few weeks. It’s a really neat programmable controller.
Uno Board
So what is an Arduino, and why would anyone want to play with one? In short, an Arduino can be thought of as a simple-to-program standalone computer. The computer is a well established one, known as a micrcontroller, and is built for the specific purpose of interacting with the real world via sensing and controlling things.
Underneath the Arduino layer is a high speed programmable microcontroller made by Atmel, the megaAVR. For the typical tinkerer to learn about and use such a microcontroller is a tall order. This is where the Arduino layer comes into play. The Arduino architechture placed this microcontroller on a predesigned PCB, taps a number of IO lines, and provides simple connections to them, and provides a power supply and communication point via USB, and an external DC power connection. The Arduino software gives the new user a simple coding interface, which is then converted to the language used in the ATmega chip, all done behind the scenes. This ends up giving the tinkere an extremely powerful, programmable package, for a low price, with a low barrier to entry.
As an example of what the arduino can do, I decided to write a “sketch” for solving a common microscopy problem. I have a camera, and a high speed light switching system. I want the camera to run as fast as possible, let’s say at 30FPS, and I want the light source to switch from one channel to another while the camera runs. This is considered “hardware device streaming”. In order to do this – I’ll tap the camera’s “frame transfer” line, which provides a TTL High signal during image transfer. This is the time when you want to move hardware, as the camera isn’t actively acquiring data while a transfer is occurring, or rather while a frame shift is occurring.
For this test I used an Andor Clara, and was able to obtain framerates of 100fps with no jitter. In order to accomplish this I used an interrupt driven method of sensing the input voltage line on the uno. If using the loop code in a traditional sense (polling mode) the litter form the timing of the loop affects the response time of the processor, and thus a timing jitter is seen in the control over the devices triggered.
If using an interrupt, the timing is FAR more accurate, i.e. fast enough that I couldn’t detect jitter when running the camera @ 100fps. Theoretically this code should be stable to ~ 500fps or so. If you’d like to try this code, it is hosted here.
Another example of what the arduino can be used for is serial communication with existing software applications. Say for example you have a program which will operate with Uniblitz shutters. The uniblitz protocol is usually one way – meaning the shutter isn;t replying back to the software as to whether or not it’s open. Because of this most programs can issue the “open” or “close” command without having an actual uniblitz controller connected. One could program an Arduino to accept these commands, and do something with them, for instance trigger a TTL driven laser to turn on. An example of some modified Serial Comm code which will trigger TTL outputs when recieving an “S1” or “S2” serial command, can be found here.
I can imagine numerous applications for this device. Motion control, illumination control, software triggering based on an input, or many otehr things. Considering how much a NI device costs, and this costs $29 complete, and is quite configurable from an open scripting code, I think this is a steal for it’s capability.
Anyone working in imaging knows that one major ongoing problem is handling the massive amounts of data collected. A relatively low resolution camera can output massive volumes of data, if combined with a stage, z motor, wavelength switching hardware or just run in video collection mode. Sooner or later, many users end up needing a storage solution beyond a laptop or carry-around hard drive.
Two typical solutions exist: Cloud Storage, and Local Storage. Now, everyone hears “cloud”, and thinks google drive or similar backup services, but the term cloud has also come to mean any storage which isn’t inside your office. To this end, one could consider the IT Department’s servers at a university to be “cloud” storage.
Cloud Storage
The advantage of storing data offsite are compelling. They usually revolve around the following points:
Offsite physical security (If the lab floods your data is safe)
Low upfront cost, as you aren’t purchasing a physical system.
Lack of required maintenance
Potential for massive volumes of storage
People outside of the facility can access cloud data easily
Depending on your facility, the costs for on site storage can range wildly. If you want a target comparison price to consider, I’d look at Goggle, which as of this writing is a cost of roughly $0.10 per Gigabyte per Month. Current Google prices can be found here. This price is not inclusive of the internet connection cost needed to upload and download whatever data you send to the cloud, so that must be considered as well.
The downside(s) to cloud storage are intrinsic to the advantages provided by offsite systems: If your data is on the cloud, it has to get there, and back to you when needed. This means the time and cost required to upload/download. For many users of complex systems, the size of one data set would take too long to move around between a lab and the cloud. So, it’s a good solution, but not perfect. In the case of inside-facility cloud storage, some of these transfer problems can be avoided, as the network speed inside of a properly equipped facility should be hundreds of times faster than the WAN connection speed, not to mention a quality IT department can establish multi-link connections between a server and a workstation to reduce transfer times.
The other consideration for cloud storage is security. Your data on the cloud is accessed by username and password. Can someone get that information? Can they obtain precious data without you knowing? For some, this risk alone precludes cloud storage for their work.
Local Storage
Local Storage is a good option for several reasons:
Your facility doesn’t have room on the IT server site for your data
Size of data precludes offsite upload/download, and you need fast local access
To ensure local physical security for sensitive data
Ongoing cost of cloud storage and network connection is too high
In the local storage realm, the most common system found today is the “NAS” server. A NAS, or “Network Attached Storage” server, is basically a computer which has one function, to store, and to serve, data to the network. These systems can be set up to work sitting next to an imaging system, basically using them as a massive hard drive, or can be configured for access on a lab-wide network. At home I use a Synology DiskStation. This system provides redundant backup, serves both work and personal files for every computer and device on my network, and does so at a relatively low cost ($500-$700 complete). My system is considered a “Personal NAS”, meaning it’s not really meant for a corporate environment, but systems like this are. These systems are a relatively low-cost option for storing large volumes of data, are physically safe if set up correctly, and quite reliable. Consider that for 1TB of Google space, you’d pay roughly $100 a month. For a $700 investment, my NAS has 2TB of storage, so in roughly 5-6 months, I’ll have recaptured the investment on my NAS. (Not considering ongoing replacement cost of the Hard Drives). The downside is that you have to administer them, meaning setting one up, buying good hard drives for the unit, setting up how much security vs. exposure is used and managing who gets room on the server. Not to mention physical security – if my house or your lab burns down, my data goes with it.
So which option is right for a typical imaging lab? It really depends on your IT department’s policies, the bandwidth of your internet connection, the type of imaging work you are doing and the cost considerations for your organization. At minimum, it doesn’t hurt to consider the options available before choosing where your data should live.
Fujifilm and Panasonic have announced development of an “organic” photoelectric conversion layer in place of a traditional silicon photodiode used in conventional systems.
Obviously it will take a while for this technology to trickle into the scientific market, but it promises another evolutionary step forward in the march of both digital image capture and cmos sensor use in scientific applications.
This is a cool attachment for the iPhone. An optical system that produces 20X-80x image magnification, and has a contained adjustable illumination source.
This is an interesting product, as it will by no means replace a stereo scope for the obvious reasons, but will allow for access to magnification by people who could otherwise not afford it or justify the cost. Nikon had a similar product a while back called the ShuttlePix, which never really caught on due to it’s price vs. market demand. This is a classic case of disruptive product innovation. The iphone provides a complete acquisition, optic, storage and transmission system with a user interface for what could be considered $0.00, as the operator can justify owning one without using it for this purpose. We all need a phone right? So what you have here is a comparison of $150 for a digital video and still capture, storage, illumination and editing system, with completely field-ready transmission capability, vs, a higher mag capable system in the shuttlepix, for “under $30,000”. For this price premium you get extended depth of field capability (theoretically this can be done using ANY focusing system), 3-d measurement (again software-based), 400x mag, and a much nicer stand/illumination system. For that $30k you still can’t snap a picture in the field of a new never before seen insect, and email it to colleagues for further analysis, whereas with the $150 solution you can.
Nikon isn’t the only manufacturer out with a portable inspection camera, each of the microscope companies have similar products, and there are specific markets where these products can be justified at $30k. But – the big thing the major scope manufacturers are failing to realize here is that the power and capability of “consumer grade” camera+transmission systems is already meeting or exceeding what was sold a few years back as a “color microscope documentation camera”. The sooner they realize this and change course to provide solutions the market needs, the better it will be for them and for customers.
Back in mid December I had the unpleasant experience of a large bird flying through my prop. In the aftermath of this event I learned that my engine had to be inspected internally, to determine whether any internal components were damaged due to the incident. My engine was due for an overhaul anyway, so I opted to invest the extra money needed to completely overhaul the engine. In the process I added an engine analyzer and a 160hp STC, to get a little more performance out of the engine at altitude. It turned out that my current prop was damaged and unserviceable, so we replaced the prop with a new one. This project was time-critical, extremely complex, and I walked into it knowing that if I received components missing one critical little part, delays would rapidly accumulate. Throughout the project I got to work with some of the people that make aviators like me able to fly, and it was greatly to my benefit.
The Dreaded call to Insurance
When I had the prop strike I knew I needed to get in touch with my insurance carrier. I mentally prepared for the usual fight with insurance. With auto insurance it’s the same old game: Avoid responsibility, haggle on repair, haggle on shops, haggle on price, up your premiums after everything is done. The last thing I was prepared for was Bill Arnold of Arnold & Arnold Inc. After about 3 hours of leaving a message with my insurance agency, I receive a phone call from Bill. He leaves me his business number, and his cell number, and his home phone number, just so I could be sure get in touch. I spoke with him, expecting the usual runaround, what I got instead blew me away. Bill’s #1 goal was to figure out a solution to my problem that provided the best safety for the future. His point was well taken, “We aren’t interested in turning a small claim into a larger one, or worse one, down the road.” We weren’t sure at the time whether an FAA-required engine inspection (i.e. teardown) applied to my situation. Bill pointed out that the insurer, Global Aerospace, would proceed with the engine teardown if, in the aftermath of the strike, I didn’t feel safe flying on the engine. This interest in my safety really changed my view of the insurer. Instead of battling out a tough ordeal, I had a partner to work with to solve this problem. Bill had a mutual interest in a safe outcome, what a thought! This approach motivated me to be fair with the insurer, and provide honest and fair quotes for the work to be performed. I think Bill’s approach saved me money, and saved the insurer money. Go figure! Ultimately Bill and I decided that the best way to determine if the teardown inspection applied to my situation was to have my prop inspected. But who could we find to do a thorough inspection the week before Christmas?
That spinning thing at the front of the plane…
I needed quick and correct answers as to whether my prop was damaged during the bird incident. Sullivan propeller offered to inspect it for me in 24 hours, the day before everyone was scheduled to take Christmas break. They could have easily pushed me to 2012, but instead they made time for me after hearing of my plight. They gave me fair and honest options, with realistic expectations on shipping, performance and pricing. I needed accurate lead times and accurate performance information in order to choose the right prop, and they nailed it. I literally had the prop in my hands the day before the engine arrived. Perfectly on schedule.
New propeller ready for installation
When I picked up the new prop, I was able to tour the extensive shop they have, and as a die hard tool geek I loved seeing the special tools and processes required for working on propellers. While in the shop they had props from MU-2’s, King Airs, Cessna 150’s and a P-51. Wrenching on this variety of props didn’t seem to phase the engineers one bit. Prop work is a rare trade, I’ve been involved in rare trades enough to know that when someone makes work like this look easy, it’s because they are a master of the craft, which these guys and gals are. For those of you who are considering what shop to use for your prop inspection, you should seriously consider Sullivan.
Engines
The well packaged accessories and documentation made detail work easier
So the toughest choice was who to use for an engine shop. Any reader of aviation publications sees ads from all over the country for engines. You get everything from people promising really low costs to groups that anodize all of the parts and give the rebuilt engines special names, trying to up the perceived value of the engine. I wanted to find a shop that could rebuild and inspect the engine in a short period of time, do the job at a fair price, and produce a result that I could trust with my life and the lives of my friends and family. This was no small decision. I investigated nearly every engine shop in my region of the country. Some had extremely high prices, others were slow to respond in offering a quote. In the process I got in touch with the owner of a shop in Corona, CA. Ben O’Con of Corona Aircraft Engines sent me a quote for inspection, and 3 quotes for rebuild options within one day of my request. Now I’m fully aware that sending quotes is a pain. People want quotes fast, but when you send it, you have to honor it. So you’re motivated to fire it off, but you want to make sure and include every little part needed for the job. Miss the part on the quote, and you’ll usually eat the cost. What I found in the end was that Ben’s quotes were 100% accurate to the invoice price. A rare thing.
Over the rebuild time I renewed my bitter hatred of commuting 130+ miles 🙂
Waiting on the engine made me realize my love for aviation is also a heroin junkie level of addiction. I couldn’t stop thinking about being back up in the air. I couldn’t stop checking DUATS, Metars and doppler sites. I’d go to the airport and look at my forlorn engine-less airplane, oh the humanity! Of course I took all of this eagerness and used it to annoy Ben with questions, updates, options for enhancements and mods to the engine. Over time we agreed to add a graphical engine monitor from JPI, as well as a 160hp STC. I view both of these mods as investments. The JPI should, if I used it correctly, help me to avoid overheating my cylinders, as well as indicate problems with the cylinders before those problems become major. The 160hp mod should allow for better climb at altitude, and a little bit better cruise speed. I was getting antsy for this engine to show up…
Install Weekend
The Engine Arrives!
For the removal and re-installation of the engine, I opted to work with my friend, mentor and uber-mechanic, Larrie Ricca. I’m a wrench turner and I love working on machines. Larrie allows me to work on my plane as much as legally possible, while giving me highly experienced supervision and advice that can only be found in a career wrench-turner/DAR. He worked to get all of the small parts ready for the install, so that when the engine and prop arrived, all we’d need is elbow grease.
Shiny new Engine!
So Friday rolls around and in the afternoon I see what I’d been waiting for: A big crate from FedEx! We quickly remove the packaging and reveal a shiny engine, with everything painted, cleaned and not a leak in sight after it’s test run. All of the accessories were packed in clear plastic containers, and documentation was well organized and easy to go through. I didn’t think about it at the time, but having all of the small parts ready to go was a major time saver for the install. From the look of things, Corona had done a wonderful job. I couldn’t wait to get the thing fired up!
Friday night consisted of installing the EDM and oil cooler. No sense working around the engine if we could do the work with it already off the plane. We had already removed the carpet and panel cover in preparation for the EDM, so the install went relatively quickly. With the EDM on ships power, we called it a night.
EDM running on Friday night
Now it's looking like an airplane.
Saturday was a long one. About noon we were ready to hang the engine. Settling the engine into the new Lord mounts was a unique experience, and a great learning opportunity. It also marked a milestone in the rebuild. All we had left was wiring and hoses! Of course this “all we had” ended up taking a day and a half. Some parts needed to be fitted as I had opted for new items like the EDM and a vernier mixture control. A half hour here and there to fit parts really steals a lot of time away from the day. In the end, I was able to test run the engine by 5pm Sunday evening.
New probes, carb, carb controls, exhaust and air intake installed.
Monday was Larrie’s final inspection and paperwork. With his official blessing and return to service, I fired up the plane and took off for the initial test flight and 1.5hr cylinder burn-in. Orbiting over my home airport, being back up in the air, and knowing that I’d had a hand in the work, was a sublime experience. The weather was good, the air smooth, and…what? I was going 10kts faster than the old engine/prop! 10kts might not seem like a lot, but consider I fly about 29,000nm of distance per year. So if it takes me 10 minutes per flight less because I’m going 10kts faster, I’m saving 48 hours per year of time in travel. That’s effectively a work-week’s of time every year!
Test run complete! Love that new engine smell…
What started as a winter flight home turned into an opportunity to meet some of the amazing people and businesses that make flying possible. I remember back in the Marines they’d say that for every infantryman in combat, it takes seven other Marines to support him. I’ve learned that the same holds true for aviation. The ability to fly, which allows me to see my family at night while working far away, to increase my business potential for my employer, and to support the growth of needed medical research, wouldn’t be possible without this team of people working so hard. Thanks to Bill Arnold for your advice and professional work, to Dave Savoie from US Aviation Finance for shuffling the payments so quickly, to Brian and Samantha from Sullivan propeller, for your humor, advice and excellent service, to Ben O’Con for your exceptional work, and to Larrie Ricca, for your mentoring, guidance and craftsmanship. I’m so happy to have the opportunity to work with all of you, and I hope others get to benefit from your hard work as I have.
-Austin
Test flight imminent
Back in the sky – thanks to everyone involved!
(Financial Disclaimer – I received no financial compensation for my writings about any of the businesses here, and write only as a happy customer who wants others to have the same results as I did.)
Canon is showing off a new CMOS sensor which it won’t really explain, but it compares the sensor to an EMCCD (3 chip) camera. The differences are amazing for color acquisition.
Once this tech becomes quanitatively measureable, it will likely push EMCCD technology into the dust bin – but, as with all of these developments, it’s not here for us to buy just yet…
I’ve been using an Ollo Clip for a few weeks now, and it’s a well established, very cool product for the iPhone. I’ve been using the 4S version, and the 5 version was also recently released.
So – why buy an OlloClip? The iPhone camera, like every other cellphone camera, is limited primarily by two things – it’s sensor size limitation (can’t change that) and it’s optics. People generally don’t want to tote around a heavy/large lens attached to a phone simply for a bit higher magnification, or wider field of view. The OlloClip addresses this by providing 3 lenses in one package. It’s a small package, easily carried in a shirt or pant pocket, yet it greatly expands the use of the iPhone. Below is an example of how the macro attachment on the clip provides extended camera capability. This means documenting things like product damage, or using it as a hack magnifying lens, are easy to do.
Macro example from Olloclip.com
On the other extreme is the use of the wide angle and fisheye lenses. Now, as a pilot one of my big beefs is that my pictures never convey the sense of perspective one feels in flight. There is simply something missing. Some of this is due to the extremely high dynamic range nature of aerial photos, but it’s also simply limited by the field of view. Sure, you can carry a big DSLR and a fisheye with you, but what about when you simply want to snap a quick pic of a cool view while in flight? This is where the Ollo Clip really shines. Here’s an example of a photo I took with the stock iPhone.
Stock iPhone Example
And here’s the same field using the fisheye lens from the OlloClip:
Way cooler Fisheye Shot using OlloClip
And I had to add a sunrise pic:
Of course, this can also present a similar perspective to any shot inside a vehicle, and it will work with video (slightly cropped down due to the iPhone’s video cropping) as well as stills.
In summary, for $60 you get a major increase in what your phone camera can do. Well worth it to capture some of those moments which will never come again.
microscopes around in every biology facility? How can it be that all these users must learn these behemoth software packages to capture some cultures? Other industries seem to have moved to workflow-based designs. You can find apps that perform full MIDI mixing on a tablet, heck, even airplanes have touchscreen controls now! Yet the microscopy industry seems to be locked into a slightly improved version of windows XP button mashup.
I recently was working on some file transfers 
I needed quick and correct answers as to whether my prop was damaged during the bird incident.
