Category: device automation

  • Starlyte Nebula Now Supports Opto Gmbh Microsocpes

    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.

  • Starlyte Nebula Adds Drag+Drop Merge Captures

    Tool simplifies manual capture

    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!

    -Austin

  • Nikon Ti-E EPI Filter Wheel

    What to look for and how to replace the drive gear

    The Venerable Nikon Ti-E remains in service in research labs all over the world. One of the first autofocus-enabled instruments deployed with the integrated PFS, there isn’t much to ask for when it comes to a modern compound fluorescent stand. For owners of the instruments, it’s important to be aware of a big maintenance item on the scope – it’s motorized epi filter cube turret.

    It lived a good life!

    These turrets use a stepper motor to rotate the large carousel into various positions. The motor, control electronics, and positional sensing system are all high quality and should last many years, however, there is an internal gear which connects the belt drive to the carousel, and over time and stress of use, these gear rings have a tendency to crack.

    I recently had a colleague ask if we could reverse engineer a solution for these, as Nikon charges a mint for them and in some cases they may be difficult to obtain depending on your region. You can see from the one supplied to me indeed had cracked, and under inspection, stress cracks from aged plastic are apparent.

    It’s important to note here that these might “work fine” under manual rotation (where the motor isn’t applying stress to the belt drive). If you are having problems where the filter isn’t moving to position, or hearing any snapping, clicking or other unusual noises, it’s highly recommended to remove the carriage assembly, and to inspect the gear closely for cracks. This is a ~ 15 minute procedure and only requires a flashlight and removal of the top cover of the carriage.

    If yours is cracked, we can supply a replacement within 1 day of order placement from our web store.

    Here is a video of how to inspect and replace the ring as well.

  • ARCLED 8 Channel LED Engine

    I’m happy to announce a new product made by ARC. Over the years I’ve worked with a large number of illuminators, from mercury excitation lamps to laser combiners. I’ve tried to combine the best traits of a light source into this device, while ignoring some of the super-awesome features that drive costs up. Key to this is to be completely flexible in LED selection. This is a “dichroic-less” device, as such, one can select as many close-line LEDs as needed for a given application. In addition, LED’s can be installed after purchase by end-users, should they need to add or modify custom modules to the system. Another great advantage for users is the ability to use a broad spectrum white channel, built into the device with the discrete LED channels. This is a unique advantage over other devices, for in many cases all that is required is a broad spectrum light source and a filter cube. Finally, due to the nature of the design and manufacturing engineering of this product, we can offer this multi-channel exciter at what I believe is the lowest price in the industry, $8,500 USD with 8 LEDs installed.

    Here’s a brief video showing the device, you can purchase it from the online store here.

  • DIY Syringe Pump

    Interesting little project.

    Not sure the money pans out considering how much time it would take to build, but if one wanted to learn mechanical control, this would be a good way to dive in!

    https://www.drdflo.com/syringe

     

  • Cooling a Pt Grey Camera

    I’ve been working with Pt Grey (now FLIR) cameras for a few years now, and one nagging question in the back of my mind has been whether or not it is possible to cool them via external means. There are basically 3 categories of cooling when it comes to low light cameras:

    • no cooling whatsoever
    • cooling to + or – some delta from ambient
    • fixed-temperature cooling to some set point.

    Of these methods, the fixed temp cooling is the most difficult to achieve, for a number of reasons, and I don’t believe these types of cameras would benefit greatly from such an attempt, so my idea was to simply answer the question, “Will cooling improve the performance of these cameras in a measurable way?”

    Normally, the cooling of a sensor takes place as close as possible to the back side of the sensor itself. In this case, I started with an already-encased camera, the Pt Grey Chameleon 3. Because I didn’t have access to the sensor back directly, I figured making contact with the case, at as much surface as possible, would suffice. In order to do that I simply used 2 l channel strips of aluminum, and placed thermal tape on all 3 sides touching the camera. The graphic below shows what was added after the aluminum wrapper. First, a peltier (thermo-electric heat exchanger) was coupled to the aluminum. From there, a large CPU heat sink/cooler was attached to the hot side of the TEC. The general idea here is that the aluminum should absorb the heat from the camera. The peltier moves a lot of that heat to the CPU cooler, which radiates the heat into the air. This is a rather rudimentary setup, but it works for the proof of concept.

     

     

    Below is an image of the assembled system. To provide the required 5V and 12V power to the cooler and peltier, I used my old reliable ATX Power supply.  This assembly low cost components from Amazon and the like. I think the total cost was $27 or so. Maybe more including thermal tape.

    So how did the system perform?

    First I allowed the stack to heat up for ~ 30 minutes. I wanted the camera to heat-soak the wrapper, so that when cooling was applied any measurable change could be collected. I think the act of adding the non-powered stack aided in the camera performance a bit, as simply having the radiator attached means that the hot camera can cool more readily from greater surface area exposure. In any case, a thermal camera was used in timelapse mode to collect the change in temperature over time. The recording was started after 30 minutes of warm-up. Images from the thermal camera were captured during a 1 hour period, while the camera was run in timelapse mode using Micro-Manager 1.4. First, here’s a GIF showing a time-compressed thermal image.

    Several things to note here. One is the large drop in camera body temp during the experiment. Another is the subsequent increase in radiator temperature, as it works to shunt the heat from the peltier. Also note the wings on each side of the camera body. They start at a similar temp as the camera body, then drop in temperature significantly (40-50°F) over the duration of the timelapse. It’s important to also note that the emissivity of the plastic camera body differs from that of the aluminum. As a result, even if the temperature is exactly the same, a slight difference in the IR image will be visible.

    Below are the results of the image captures. First is a graph showing maximum measured intensity of any pixel in-frame, over the duration of the timelapse (120 frames @ 30Seconds interval). In the case of “hot pixels”, as the camera temperature decreases, the collected signal from those pixels drops.

    Graph of measured 8-bit maximum intensity in image over time of experiment. Orange line represents a 20 point moving average trend.

     

    Next, I wanted to measure the total # of hot pixels. Now, it’s somewhat nebulous to define a hot pixel, but I used anything 1.5x greater in intensity than the minimum background, or offset, of the image. On this experiment, the average background was ~ 14, resulting in a threshold of 21. I was really surprised by this one. There is a rather large spike in the data, and I’m not certain what that is from. However, this again shows that the cooling is indeed reducing the hot pixel count, as would be expected. Additionally, the count can be seen to normalize at around 1500 pixels, which I expect is where the system started to thermal stabilize.

     

    For a final set of interesting images. Here’s a shot of the stack after the experiment finished. Note the low temp of the wings and the back wrapper block.

    Another interesting shot, this one of the sensor face. Using the cooling system it was at 104°F.

    Turning the system off produced a temp of ~ 130°F.

    My conclusion is that it is possible to cool even encased cameras using external cooling methods, to improve the performance of the camera(s). I do not think such adaptation will yield comparable results to a camera designed with cooling from the start, but this is an interesting option to achieve better results from a camera with a low price point.

     

    -Austin

     

     

     

     

     

     

     

     

     

  • Data Logging in the Cloud

    I’ve been working on a project which requires data logging from a mobile device over several days. I came across a neat site which supports simple uploading and view/export of data, from numerous sources. It’s called thingspeak.com.  Once you have data loaded into a channel, there an excellent tool which supports the execution of Matlab code on the data. You can even display the results of your matlab calculations in the channel window! There’s also an “Act!” ability, which allows you to set up reactions to thresholds and so forth.

    Thingspeak seems tailored for the IOT world, but this is a compelling opportunity for biologists, who may want to log environmental data into an easily displayed cloud location.

    Here’s an example of the channel I created, and below is an iframe object, which shows the most recent measurements made, dynamically!

     

  • A serial monitor that works in Win7x64!

    David Biggs at KB Imaging LLC put me onto this serial monitoring software, called SUDT Accessport . I’ve used it a bit for some work on the triggerscope, and it works very well! You can watch data transmitted between USB emulated serial ports, under RS-232, and it will output the communication in either ASCII or HEX. I hope others find a use for it!

    -Austin

     

  • How to use external triggers on scientific and industrial cameras

    Controlling a camera from an external trigger can be very useful. External triggering provides greater timing accuracy, direct control over exposure duration, and remote operation from TTL devices. This is a prime reason I made the Triggerscope controller, so I though it would be useful to explain how this works and what you can do with it.

    What is “triggering”?

    Most cameras built for scientific imaging or life science have a high density connector located on the back. 90% of the time, this is only used by savvy customers, or OEM integrators (companies buying a camera to place inside a machine for resale). The connector on the back of the camera will typically include 2 basic functions: Inputs (connections which send signals into the camera) and outputs (signals which activate when the camera is in a process or cycle).

    Why use Triggering on a camera? Doesn’t the software control image capture?

    Of course, software can tell a camera to snap an image. But when will that image be captured? Software needs to do more than say “snap” when you capture an image. Behind the scenes, a LOT of stuff happens!

    • the top level controls you see are converted into camera-specific commands via the camera “device driver” in your software.
    • The camera commands are fed into a control card or USB port and up to the camera.
    • The camera accepts the commands, which activate sets of tables in the camera firmware, to set up a sequence of turning on and off clocks and transistors at very high speed, all depending on your binning, ROI, etc.
    • The camera performs the above operations, and sends back an image.

    What is quickly apparent is how much has to happen to get an image. In addition, the camera firmware will process some instruction sets faster than others! So some exposures might come back 200ms from issuing the “snap” button, while others will return in 130ms, 30ms, who knows!

    So when precise timing is desired, and you really want that camera to fire at a specified time, triggering may be used. In this configuration, all software comms with the camera are pre-compiled, everything’s done. All of the steps above are performed, but the last step, the “camera performs operations above” sits….and waits…for the trigger line to run from 0 Volts to 5 Volts. As soon as that happens, an image is captured.  For single frames, this is somewhat useful, but for sequences, this is great. We can capture images at some interval with 100% confidence timing is accurate.

    Example

    Let’s look at a typical camera, and pull the information we need from the user manual, in order to better understand triggered control. For this post, I’ll use the Photometrics CoolSNAP MYO camera, and as Photometrics makes it easy to read up on the user manual for their products, you can find the user manual here.  Page 21 of the PDF describes the various operating modes for the trigger input. Note, the PDF also gives us information on EACH PIN used in conjunction with input and output signaling. There’s more than one!

    Screen Shot 2016-01-15 at 2.33.15 PM

    Note, PM also provides short descriptions for each pin:

    Screen Shot 2016-01-15 at 2.33.29 PM

    So – now we know which pins communicate which functions from the camera head connector – to connect to any of these, we’d simply connect a ground wire, and a positive pin wire to our chosen camera pin (for our needs, say Pin 1 – Trigger In)

    Now – the most pertinent for us is the trigger in line, which runs in a few modes.  Let’s review each, and why we might use them:

    Trigger-First (sometimes called other things like “Fire”)

    In this mode, the camera is set to snap some # of images (let’s say 10), but waits for a trigger input. Once that input goes high, the camera snaps 10 images as quickly as possible.

    Strobe

    In this mode, the camera is again configured for some # of images, but every image waits for a trigger.

    Bulb

    In this mode, the exposure time for each image is controlled by the input trigger. Again, multiple images are assumed (although Image qty of 1 is acceptable), and each frame waits for a trigger input pulse.

    These three modes constitute the majority of uses for a typical triggered input line.

    So, what does “receive a trigger” actually mean? Good question!

    Triggering = TTL Control

    Cameras, like almost all computer systems, are made to interact with external systems. One of the oldest, and most common methods, is referred to as “transistor transistor logic” or TTL. This boils down to the concept that if we specify an electrical voltage value of X as “off” and Y as “ON” then we can remotely flip a switch.

    Many imaging devices use this communication method. A simple uniblitz shutter for example, can accept USB/serial data to open and close the shutter, but using TTL is faster and simpler. (just one thing to do, send 5Volts or 0Volts.) Below is an oscilloscope capture of such a signal. The vertical scale = Voltage level, and the horizontal scale from left to right = time elapsed. My annotations are in red. Note the yellow line, which indicates the signal.

    ttl_example

    Example Signal

    Let’s say we have a device, for now, it’ll be the triggerscope 2, which is connected to the “TRIGGER” line of our camera. We want to signal the camera to capture immediately after we turn on an LED. In this case, we might use the triggerscope line 1 for the LED on and off, and line 2 for the camera signal.

    In our software, we’d specify the camera exposure time, binning, and other usual parameters. In our controller, we’d set the output to high when we wanted to capture our image. Let’s use an example of 1 image:.

    Tell the camera to acquire using software (nothing should happen yet!)

    -Camera waits for a trigger signal

    Tell our triggerscope to send a TTL high

    -Camera captures an image.

    Tell our triggerscope to send a TTL low

    (nothing changes)

    The above sequence can be used for a series of images. In that case, the acquisition would be configured for some # of frames (say 10), and the camera would capture 1 frame each time the signal swung from low to high.

    To tie everything together, I’ve recorded  quick video explaining this on the scope. Check it out!

    [youtube width=”600″ height=”365″ video_id=”4KNe5GxpuOo”]

    So – now you know how cameras can be controlled via TTL – if anyone has questions please comment below, so I can address them. Thanks!

    -Austin

     

     

     

  • Acquisition Speed Comparison of MetaMorph, NIS Elements, Micro-Manager

    How fast can a typical imaging system really run? What factors affect this? While most research might not require rapid sequential capture, almost all experiments can benefiet from tight exposure/illumination timing, yet few microscope users are aware of timing delays injected into experiments by the control software they are using. So how much delay is caused by software? I’ve long wanted to look into this, and finally got the chance!

    In order to accomplish this, I programmed a microcontroller to accept commands from the Lumencor Spectra-X. This high power/high speed LED engine is popular for fluorescent excitation, as a result, almost every available software application can control it. I set up my code to measure the time in which a known shutter, or known wavelength command was received on the serial line (well, USB serial).

    The team at Technical instruments were kind enough to loan me the use of their equipment, so a generous thanks to Reese Allen and the entire Technical instrument staff!

    Experimental conditions were as follows:

    • All software packages were installed on a clean OS install of Win7/x64
    • Test machine was a Dell Precision series
    • Tests were performed by configuring the camera to run ~100fps. This was accomplished using a 4×4 binning, and an exposure of 9.8mS.
    • All software applications were set to send at minimum one shutter and one wavelength change per acquisition cycle. (i.e. 1 picture from the camera, + 1 wavelength change + open shutter, then switch wavelength and cycle shutter).
    • All applications were first tested in a “free run” mode, to confirm the camera configuration was capable of 100fps at minimum.
    • No other devices were installed for these tests.

    The results were quite interesting:

    Software
    NIS Elements V4.30
    Micro-Manager V1.4.22
    Metamorph V7.8.12
    Metamorph Streaming
    Average Overhead
    60mS
    71mS
    65mS
    11mS
    Max FPS
    16
    14
    15
    90

     

     

     

    Here are some videos showing each of the programs performing. You can see some timing variation (likely caused by my capture device) but the averages are easy to resolve, and they correlate to the speed seen on the captured image stacks.

    NIS Elements

    Micro-Manager

    MetaMorph

    What becomes quickly apparent is the influence of asynchronous device control using metamorph’s “Stream” function. This is making use of a patented computer-based device sequencing technique. This technique waits for a camera “event flag” (interrupt) to fire, and when it does, a pre-defined set of events occur which control devices. This is similar to what many external trigger devices do, such as a configured national instruments card , or a pulse oscillator, or the triggerscope. The key difference here is that an external card and/or device isn’t needed, this occurs within the PC itself.

    Some further thoughts:

    • Micromanager is a great open-source competitor to other pay-for solutions. Good speed performance for a low up-front cost! (the cost of setting it up!)
    • It’s interesting that this never really seems to come up for 90% of customers who purchase “high speed” devices. Either the exposure times needed for acquisition of dim signal are so long as to never reach the speed thresholds shown here, or the capture frequency needed for a given study doesn’t require these speeds, or some other cause, but in my experience this is rarely a complaint on behalf of clients. Why isn’t this a bigger problem?
    • Many, many devices can’t reach the speeds shown here. In my tests I was using an LED driver. LED’s should have a switch time in the <5mS range. The slowest components usually found on a common automated microscope are the filter wheels and turrets, which usually run at the 50ms range when fully loaded with filters. (that’s on the fast side). So is this the reason the problem isn’t exposed more often?
    • By far, the slowest components you’ll find for microscopy are found on automated microscopes. Shutter open/close times on a common scope (i.e. big 4 name brand scope) can be in the upwards of 100ms! Moving a big filter turret usually takes 200mS. Again, this begs the question of how important speed really is for the common researcher….
    • For those who want the fastest possible speeds, have no fear! I’ll be announcing some major improvements to my triggerscope soon, to include programmable high speed sequencing capability!

    -Austin

     

     

     

  • Sub $2 microcontroller solution

    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.

    IMG_4253

     

    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.

    -Austin

     

  • Countdown to a Revolution in Microscopy – Day 3

    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 requiring any 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.

    Modern design for microscope components makes control simple and efficient.
    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 🙂

    -Austin

     

  • Nikon nSIM wins #5 in TheScientist’s 2011 Best and Brightest

    Here’s a short video review of the top 10 innovations in 2011. Some really cool technology here!

    Top 10 Innovations of 2011 from thescientistllc on Vimeo.

  • The CNC Machine is done!

     

    System completed, ready for a spindle.

    So after 6 months of watching the guys at mydiycnc complete their manual, and roughly 4 months of building, I’m happy to post that I’ve finished the machine. I’ve written an extensive post on the last few days of building, on the build log here.

    I couldn’t have completed this project without the major helping of patience by my wife. Thanks Jenny! (I think the boys are happy that the “robot” is all done).

    Thanks to my business colleagues (Carey and John) and friends at Sutter and ASI for your advice and support.   It’s amazing how much I’ve learned from you! Of course, thanks Stephen for coming up for this project and for your email support and advice!

    -Austin

  • Lumencor Sola Driver for NIS Elements

    Yesterday we received our first shipment of Sola white light LED driven sources for microscopy. I had a chance to snag one and write a driver for it. Price is $300 USD. The driver controls both the shuttering and  ND on the box, and integrates easily into Elements as a shutter and ND filter wheel.

    Please contact me if you are interested!

    -Austin

     

  • How to Align a Dualview 2

    Walking through the alignment procedure of the DV 2, narrated by Jeff Harris from Photometrics . Great video and great explanation Jeff! For those of you who have a DualView, I’m certain this video will come in handy.

    httpv://www.youtube.com/watch?v=WJC5_DdaH80

     

  • Acquisition crashes, and power settings in Win7

    Windows 7 has a new power management interface, and the design of modern motherboards, along with win7 Automatic Power Management (APM), can cause some insidious device-based software crashes if power options aren’t set correctly. Here’s how to make sure your system is running in the best mode.

    • Open the Windows Control panel
    • Search for and open “Power Options”

    • You’ll see a “power plan” like the one below. Click the “Show Additional Plans” button, and check the radio button for the “High Performance” plan.
    • Click on the “Change Plan Settings” link, then click “change advanced power settings”.  This window is where the real control over the power plan exists.

    • Browse through each item provided, and set power management to either disabled, maximum performance, or off, depending on the item. Things like turning off the hard drives are a bad idea on an acquisition system, as this can cause problems with long term timelapse.
    • One key item is the PCI link state power management. This should be set to “Off”. This item selectively disables power to the PCI bus. Some of the cameras and devices used in acquisition systems rely on PCI / PciE based cards to operate, and cutting power to these cards can cause all sorts of havoc.

    • Another common problem, probably the biggest I’ve seen, is the USB suspend entry. Again this function turns off the USB bus when not in use. This has caused crashes in software when operating USB devices, so it should be set to “Disabled”.

    • Once you’ve investigated each item and made any desired changes, click OK, and then close out of the power option windows.

    Making the changes noted above should make a big impact on the stability of your imaging system. Hopefully this guide helps you to avoid acquisition crashes on your system!

    -Austin

  • Voltage output from NIS Elements, MetaMorph or uManager for under $200

    USB-6008 connected to my multimeter

    I posted briefly about this a while back, in my explanation of the demise of the parallel port. I finally got my hands on a National Instruments USB-6008 box, and have found the unit to be 100% compatible with any NI-DAQ controlling application. What follows is an example of how to set this up using NIS Elements.

    First – what types of devices could be controlled with this?

    • AOTF Controllers (Spectral, Neos, Etc.)
    • Single Shutters (Uniblitz Etc)
    • Piezo Z Controllers (ASI, MCL)
    • Directly driven 0-5v lasers
    • Monochromaters
    • LED Light Engines (Lumencor/89 North)

    So – this thing is great when compared to the PCI cards normally used for numerous reasons:

    • Cost – This is ~$160 USD, vs. the PCI/PCIe cards running $1,500+
    • Size – This box is quite small, doesn’t require a huge cable or breakout box, and doesn’t occupy a slot on the PC
    • Portable – this will work on a mini form factor PC, or a laptop (which is what I used for this post), instead of requiring a full size tower

    Installation:

    Install is a snap. The only hard thing to do is place the pin indication stickers in the correct orientation on the box. If you mess this up you can always refer to the manual, but the little sticker strips included with the box make field-modification much easier. After this run the NI installer and reboot. Finally, connect the USB cable. The box will appear, and if you like, you can launch one of the NI test apps to run the device.

    In Elements, we’ll re-run the installer and check the “National instruments” hardware group, then select “NI DAQ”.

    Next, open Elements, open the devices window, and add the NI Device.

    Once we add the device, and click configure, we can define what each of the inputs and outputs do. Here I’ve selected a 2 line AOTF.

    After you’ve dialed in the settings you want, close the window(s) and if you don’t see the new device control panel, right click and select “acquisition controls” to find it. In my case the AOTF Settings window popped up after closing the device window.

    I also  made a short guide to using this box in elements via the Youtube video below. ***In the video I mention this thing costs $130, which is incorrect. It’s listed on the NI site as $168 as of today. Also I have yet to test more than 1 unit, but will be doing so shortly…

    httpv://www.youtube.com/watch?v=poKZjRgWdhQ

    One point of discussion is devices that require a 0-10v range. I’m looking into using a small powered op-amp chip and maybe packaging it into a small box for sale, or at least I’ll write up a how-to on using one, for people that need this voltage range. Luckily most of the devices out there can accept 5v or 10v input. Overall I’m happy to see NI is moving beyond PCI and PCIe bus cards. USB based boxes like these lower the acquisition cost for the customer, provide everything we need in the life science world concerning speed, and open up access to a wide array of devices. I’m looking forward to using this box on future systems!

  • ASI MS-2000 Flat Top Stage

    Apparently ASI has had a flat top variant of it’s MS-2000 stage available for a while now. News to me! If it’s anything like the current stages they sell I’m sure it’ll be a frequently recommended product from me.

    – Austin

     

  • Nikon DS U3 Series Controller Install Guide

    DS-U3 Controller

    The new Nikon controllers for DS Series Cameras run on Firewire. As with other firewire adapted imaging cameras, there are numerous

    small issues to awtch out for during the setup and operation process. Once they are up and running, they should be fine – but for those of you who perform installations, you’ll probably find this info handy:

    Here’s the Install Guide for the DS-U3 controller. Follow each of hte steps included to insure a correct installation of the unit.

    – Austin

     

  • Photometrics LVDS cards on Win7

    I recently slogged through a tough install with a customer (Thanks Sean!!) in an attempt to run an older Photometrics camera using a PCI card in windows 7/xp. What we found was that the latest driver, (as of this post v. 2,7,10) is not working with PVDS cards! The solution for now is to roll back one version earlier, then things should be OK.

    You can basically tell if you’ll be affected by looking at the cable attached to your camera. an LVDS cable looks like this:

    LVDS Connector

     

    – Austin

     

     

  • *UPDATED* Micro-Manager Tethered to a Nikon Digital SLR

    ***UPDATE 3/3/2014***

    After a few requests for a report on x64 capability using this tethering technique, I tried installing the NK Remote software on a rather fresh copy of Windows 7×64 – it did not communicate with the camera at all. On the other hand, the open source application “DigiCamControl“, worked perfectly. Now, as far as micro-manager goes, there isn’t a connection from DigiCamControl to micro-manager. So – short term solution is to run the proposed setup below on an x32 system – if anyone gets x64 working please post here!!! -Austin

    So I had a customer interested in a macro application for scanning. In some cases, applications like these don’t require a telecentric optical system such as the AZ-100, nor do they fit into a typical stereo microscope application. So, what to do? Well, when your object for imaging is too large for a microscope, one option may be a macro lens on a digital camera. Something like this:

    Copy stand for SLR

    This type of system will allow for a stable focusing and zoom setup, but is limited in magnification power and light control. In some cases though, this is the way to go.

    The next problem is that of focal and positional control. No microscopy device control software available, such as elements or metamorph, supports non-scientific grade cameras. So, how do we position a specimen under this camera in an automated fashion? Well, it turns out micro-manager has a plugin available for such work, and it’s available in the nightly builds here .

    What you end up with is a camera that can be controlled from a laptop, along with a stage, z motor and other automated imaging hardware. Here’s an example of my setup running on a windows 7 x64 laptop and a D80.

    D80 and Win7 x64

    Requirements

    This setup requires the following items:

    1. Suitable camera and lens (see below)

    2. Copystand for camera.

    3. Computer for control.

    4. External power supply for camera or a battery extension (more for ease of use but I consider it a requirement).

    5. USB Cable to camera.

    6. Control Software for interfacing to uManager. This is pay-for software, found here. The software currently ranges from $90-180.

    7. A right angle view finder isn’t required, if you don’t mind a stiff neck!

    Setup:

    So, follow the instructions found here for setup. My summary of setup, which took a whopping 5 minutes (this is amazingly quick for open source software!) went as follows:

    1. Download Breeze Systems trial for NKRemote & Install.

    2. Download nightly uManager build & Install.

    3. Set camera to PTP mode.

    4. Run NKRemote and snap image to confirm communication with camera.

    5. Run uManager. Edit hardware seup using the “Setup hardware” tool and removed the demo camera, and added the NikonDSLR.

    6. started snapping images! Here is an example of running in uManager (click on the picture for a higher res version):

    Nikon D-80 acquiring images in uManager

    What cameras are supported:

    All of the basic DSLR models from Nikon are included with the NKRemote software. Tethercam is the driver used for the uManager side, and it states an “incomplete list” of cameras as follows:

    Nikon D7000, Nikon D90, Nikon D5000, Nikon D300, Nikon D300s, Nikon D700, Nikon D3X, Nikon D3s, Nikon D3, Nikon D200, Nikon D80.

    Lenses to Use:

    Some lenses that work as portrait lenses like a Nikon 50mm will work adequately as macro lenses. On the other hand, it’s recommended to shell out the extra cash for a well-made macro lens, such as this one. The nice thing about working with commonly available photo gear is that in many cases you can even rent lenses to see what works best for the job at hand.

    This was a fun and quick test and I am excited to see how this capability is used for macro work in the future!

    -Austin

  • Parallel ports wont work in 64bit windows!

    After speaking with several software vendors I’ve learned that win 7 64 bit will not operate a parallel port with any device automation software. So gone is the ttl access needed for so many of our devices! Fortunately there are low cost alternatives. The guys at metamorph recommended this national instruments io controller, which sells for $115 out the door. Not too bad of a deal, and you get a cleaner method of cabling and interface.

    http://sine.ni.com/nips/cds/view/p/lang/en/nid/201630

    Both meta an elements offer Ni drivers, so this should be a simple switch from an old parallel based system.

    It’s important to note that this won’t solve the issue of parallel-based communications on devices where they only connect via parallel. It’s important to check with your device manufacturer(s) what options are available before simply chucking your old pc!

    – Austin

  • Instensity Calibration using a Photostable Light Source

    Camera Calibration Source

    I’m very excited to announce Technical Instruments’  first ever camera-specific calibration product! At left is an image of the CC-560, or Camera calibrator, which emits photons at 560nm.

    All of the cameras in the microscopy world rely upon a single defining point that (theoretically) justifies the price premium we pay for them. That defining point is reproducible, quantitative linearity of intensity. Put simply, if I acquire some number of images, using the same camera settings, over a long period of time (days, weeks months etc), my camera should give me image intensities with the same brightness values, when provided the same amount of input light.

    Note that linearity, as well as quantitative accuracy, are expected minimum specifications on camera info sheets. Some examples can be found here:

    Nikon DS-Qi1

    Andor Clara

    How does this quantitative/linear capability translate into real-world data for the end user? With difficulty! Upon purchasing a new camera, most new owners of a quality camera will find a unique set of conversion tables for their serial number camera.  These tables note in part the individual electron to ADU conversion rates for each A/D readout speed, and Gain setting. This data can be used to discover how many electrons the camera collected for a given image. For instance one could have a  3.05 e/adu conversion rate at 10Mhz, as well as a 2.54x gain setting. Using these conversions we would find that a reading of intensity in an image, say with a value in the image of 100, would convert to ((100/adu)/gain) or (100/3.05)/2.54 = 12.9 electrons collected. Note this basic calculation does not include bias offset, which is another value provided in each camera’s specification sheet. The take home point here is that each camera manufactured will have it’s own, unique, set of values. You can use these values to convert your ADU’s (Analog to Digital Units) which are what you see as intensities in your image, back into electrons collected on the camera. This is especially useful when comparing images collected between multiple gain settings, or where camera speeds were changed and a corresponding change in image intensities was noted.

    For some people, these series of calculations and corrections, as well as others, may be a required, however tedious, fact of life. On the other hand there are a vast majority of researchers who want answers to simpler questions, such as:

    • What is the comparative sensitivity difference between the camera I used to work with in the lab down the hall, and this new camera I am now using?
    • How do changes to my camera, such as binning, really affect my data?
    • What do the detailed controls do on my camera? (Such as changing “Clearing” settings, or Parallel Clock speeds and voltages)

    Customers using EM-CCD cameras may have additional questions, such as:

    The simplest answer for these questions was to have the customer find some photo-stable light source, and use that light source on the microscope to find the answer. The tough part was actually finding a useful photo stable source! As an answer to these challenges, a few colleagues and I have created this product, available from my employer, Technical Instruments.  This calibrator is designed to give people simple and direct answers to these types of intensity based questions, with a minimum of hassle or headache. The product will work on ANY C-Mount camera, and can be used either for dedicated-use calibrations (i.e. install – calibrate – remove) or can be placed in between the camera and the microscope in a permanent installation (See example image of Andor camera and Nikon Ti-E microscope with CC-560 installed at right). I’ll be posting more soon on what this product can be used for, however I’m certain there are numerous uses for this that we haven’t considered. Please take a look at our new CC-560 Camera Calibrator.

  • SLR cameras for Microscopy

    Camera on Leica Microscope

    Most of the time, I work with people who need measurable and accurate (quantitative) results from the images they obtain. While this constitutes the bulk of my daily job, there is a much larger group of people using cameras on microscopes for photomicrography. Or put simply – taking a picture of what you see through the scope for the

    purposes of presentation or archiving.These people live in an a space completely underserved by the microscope imaging community. Here’s why:

    • C-Mount cameras are usually cooled (which isn’t needed for basic trnasmitted image capture)
    • C-Mount cameras are usually specified to be linear and quantitative (again unneeded for basic image capture)
    • The software used by these cameras has more features than are needed to snap an image
    • The production rates for these cameras and cost of scale equal an unjustified high price for basic image capture.

    Now when I use the term C-Mount camera I’m referring to cameras that are dedicated for microscopy use, which have no glass lens assembly in front of them, and connect to the scope using an ISO C-Mmount.

    So what options are available besides the traditional camera? Enter the venerable SLR. Before the digital camera era, everyone had a film body camera on their microscope if they were acquiring images. This system could produce beautiful images, but required all the usual steps in film photography. There are a wide array of mounts available for cameras such as these, as most miroscope optical systems were designed to work with SLR cameras at some level.

    Today there are a wide array of DSLR (Digital Single Lens Reflex) cameras available. These cameras use similar (but not exactly the same) optical setups that will, in most cases, work quite well on a microscope. Why is this?

    • In general, we don’t want glass to be in front of the sensor. DSLR cameras, like C mount cameras, use a lens connection, allowing for the lens to be removed, and the camera to be placed on the microscope. So the microscope becomes the “lens”.
    • Modern DSLR cameras like the D90 from Nikon or the 50D from Canon include a “live view” function. This function allows the user to view the live image from either the camera body, or the method I recommend, through remote control software running on a computer.
    • DSLR cameras include incredibly powerful image processors in-camera. This means you won’t ahve to fiddle as much with white balance to get a high quality image that accurately depicts what you see under the scope. Pathologists are famous for seeing these color balance errors as they have the best trained eyes when it comes to minute color change on stained specimens.
    • Unlike film or digital still cameras, newer DSLR cameras can acquire HD live video. Here’s an example from a Nikon camera. One can imagine the use of this for live microscopy recording, all with the same camera…

    httpv://www.youtube.com/watch?v=DPJVfztNMJQ&feature=related

    So why not use any handheld camera? Because the typical lower cost camera will not allow you to remove the lens assembly. This is the primary benefiet of DSLR and C mount systems.

    If you’ve read this far and are interested in using a DSLR for your microscope, you’ll need a short shopping list of components on order to make everything properly work. Here are the components you’ll need:

    1. Camera Body (you don’t have to buy the camera with a lens if this will be a dedicated scope camera)
    2. Camera -> Microscope Mount system.
      1. You can use either a microscope manufacturer’s recommended system like the ones described here (Nikon F Mount options)
      2. Or use a high quality aftermarket adapter from a company like this (Canon and Nikon F Mount coupler)
    3. Control Software for your camera (Nikon uses software that you have to buy separately, canon software is included with the camera).

    Notes on Acquisition:

    Once you have the parts together, you’ll need to set the camera up for the right shooting mode. On most cameras you’ll see an “M” mode. This is preferred for microscope use. M is full manual mode. There is no focus or aperture for the camera to control on the microscope, so those adjustments are not required. The remaining adjustments (exposure time and ISO) can be controlled manually. For low light fluorescent work, use high ISO. For normal transmitted light, use low ISO. You can use the metering system on the camera to determine the exposure time, and all of these settings can be controlled from the computer. Finally, make sure to enable “exposure delay” mode, which will avoid capturing any vibrations introduced into the scope when the shutter drops open!

    As always if you have any questions on this technique you can contact me with questions!

    – Austin

  • Micro-Manager 1.3 and Velleman Boards

    If you are running micro manager and need to control a device via TTL or voltage, there is a nice driver written for umanager along with an inexpensive A/D card. The Card I used for a recent project was the Velleman K-8061. I’ve written up a simple how-to on connecting the board to a windows PC and getting umanager to run it.

    Setup instructions for the Velleman Board and uManager 1.3

    uManager Wiki on the K-8061 board

    Velleman Board Link

    -Austin

  • Elements 3.1 Released

    Nikon has released it’s major revision of Elements in version 3.1. (Build 587). There are several new features in this build and from what i’ve seen it’s quite stable. You can download the build here.

    – Austin

  • What can programming macros do for me?

    I’ve been running into a lot of programming applications lately. The fun part about using the Elements (or other) programming system is the amount of utility and flexibility it can offer to end users. Most people think about programming in our industry only as it relates to image analytics. I wanted to point out some other things macros can do for you:

    Acquisition & Device Automation

    Do you have a stimulus device or method you want to trigger from your acquisition software? Almost every device on the market (FRAP illumniators, Profusion systems, heating systems, electrical signaling systems) can accept a command input from TTL. You can use Elements (or other software) to control the parallel port on your computer – giving you control of the device you already have. A macro can tell the device to start, stop, adjust a setting and can then record that command into elements (i.e. at what time point in a timelapse the command was issued).

    User convenience

    Are you always pressing the same buttons in software to control the microscope? You can use macros to assign keyboard keys to run special functions. For instance when you press the “0” key on the number pad you can make the microscope load a “DAPI” illumination setting and acquire an image.

    User interaction

    Do you only run a few experiments over and over? You may be working harder than needed by re-configuring your software to image with a specific protocol. You can use a macro to configure all of the settings you want in one operation, and then dial in specific changes you may want to adjust before acquisition.

    In general any button you press, number you enter or menu you click can automatically be performed inside of a macro. Keep this in mind any time you are repeatedly clicking on the same things and slowing down your work!!

    EXAMPLE DOWNLOAD
    You can find an example macro for use in Elements here. Open Elements, open the Macro menu and click Edit (or press F8) and copy the code from this page into the empty macro. Then just save and run it!

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