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.
How well can modern AI agents produce engineering designs for optics? Well – I wanted to find out.
To test this, I’ll walk through my goal. I need to get a lens made and I need it fast. I also need it to work properly. Lastly, I need it to be manufacturable at scale which means using glass substitutes often found in China.
So – using Claude Chat, I took performance specs from several existing lenses, handed them over and added:
“Make me a lens design that meets these general performance criteria.”
I also asked :
Use Chinese available glass (e.g. K series)
Validate the design using a raytrace
produce estimated performance data
produce design drawings
produce a prescription
produce a ZMX file
Here is the design it produced, it sure doesn’t look bad so far!
After a while it decided to build it’s own python analysis tool using multiple metrics, it did the job and generally things look ok. However – is this actually OK? Let’s drop the lens design into Zemax.
Using a COTS 200mm doublet as a comparison, I pulled a image, plot, ray fan and Huygens spot to inspect. All look quite similar, the spot size can be realized a bit better, but consider the aperture on the reference file was slightly larger, so that means difference in NA.
AI Doublet Left — COTS Design at right
Ray Fan Diagram
Note there is a difference here, this design is not optimized – with an optimized second surface, it’s obvious a lot of improvement can be made. Yet for a commercial type lens, I think this is a good example of a sufficient result – it’s less than the diffraction limit, which is a suitable bar for pass failure.
Huygens spot size is below, again note the difference in the psf due to optimization missed.
Finally, we can compare the simulated image formation – here I don’t think there is a clear winner, which is what we are shooting for in a commercially produced result. Very cool.
Compact, Simplified TTL and DAC – Micromanager Native
I’m happy to share a new device I’ve been working on after encouragement from numerous clients. This new smaller version of the Triggerscope is intended to bridge the gap between large complex systems and more streamlined setups.
With the Mini you get:
4 TTL Outputs at 5V
2 DAC Outputs at 5V
1 3.3V to 5V input Trigger
Status LEDs for all connections!
A single USB-C Connection to the computer
Full supported Micromanager Triggerscope-Hub Behavior
This was a super fun project for me, as for the first time this board uses a bare MCU, which enabled my team to use any connector we wanted (hence the USB C) as well as full USB-Serial emulation on our own terms.
I’m also quite fond of the baby side-emitting LEDs on the outputs. These LED’s draw almost no current, but having them for all of the outputs makes it so easy to know whether a given control line is on or off. For the DAC LED’s, they change brightness with the output!
I tried to keep this design in-line with the current TG4, as it’s worked well for us over the years. This one is of course thinner, lighter and smaller, but in effect a truly miniaturized version of the larger model.
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!
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!
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!
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.
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!
While I haven’t had a chance to test these for accuracy, I was excited to find them while looking for some tube lens specs! You can find the file set here. These designs include some of the common infinity corrected objectives, as well as tube lenses, from every major microscope manufacturer.
Kickstarter has another iphone microscope project, this time it looks like an attachment which includes a 4 line LED, focusing and optical element system, and machined body. Looks cool!
Over 450 years have seen the compound microscope evolve into an incredible instrument. From simple contrast viewing, we’ve moved to super resolution systems capable of sub-diffraction accuracy. But for all this advancement, we’ve been stuck with the architecture of the microscope platform. Over 70% of labs end up buying both inverted and upright microscopes….until today!
I’m happy to introduce the Revolve Hybrid Microscope! A scope that combines both inverted and upright observation into one instrument. I’ve worked in this industry for over a decade, and this is by far the biggest evolution in the idea of a scope I’ve ever seen! I’m so excited to share this with the research community, and I hope you’ll enjoy learning more about it!
The Concept
We all know that uprights and inverts use similar objectives, illuminators, position systems and cameras. Why duplicate all of these expensive components? Can’t we find a way to merge these two systems into one unified instrument? Echo Labs has done just that, with the Revolve.
As you can see above, this a completely new way of approaching what a microscope should be! The revolve is two microscopes in one. It provides a fully capable inverted research instrument, AND a fully capable upright microscope, into one device. So the revolve is 2x the microscope at 1x the price, size and maintenance. While the revolve brings so much more capability, it’s also less, in all the ways less can be good. You’ll note the lack of a tower computer. It’s gone! The integrated iPad drives everything inside the scope. No more rat’s nest of wires on your lab bench. Of course, with the iPad, training isn’t required for new users. Both my boys (6 & 7yrs old) got a chance to use the fluorescent side of the app, and were capturing multichannel fluorescence with a few seconds. Using the touchscreen is simple and an easy extension to the other controls on the scope, so the keyboard and mouse won’t be missed. You may also note a lack of wires. In normal marketing pictures microscope manufactures won’t connect all the boxes, so things “look clean”, but the revolve IS clean. Only 1 power wire is required for operation, and all of the other brightfield, and fluorescent components are placed inside the body of the scope! To see these functions live, Echo Labs has produced a great website which includes demonstration videos, at www.echo-labs.com
The Revolve Microscope
Let’s get right to the specs. This is a compound, infinity-path microscope. Current glass selection includes the entire line of Olympus objectives, with everything from long working distance phase to high NA oil immersion lenses. Both a high NA and long working distance transmitted light condenser are available to support phase and brightfield. The instrument uses the Apple iPad for control, interface, storage and display of images. The body and chassis are designed to be compact, fitting inside a fume hood or a lab bench with shelving installed. A single power supply runs all internal components, so there is only a single power connection required, and aside from that, no other cables need to be connected.
Brightfield
In brightfield mode the iPad camera is optically coupled to the lightpath, providing sharp, color balanced, auto exposed images. Optical coupling is set to provide the full objective field within the iPad camera FOV, with pinch+zoom available should the user want a traditional square view. On-screen controls are provided for color balance, brightness and contrast.
Due to the unique nature of the upright/inverted combination, both high res close working condensers as well as long working distance phase condensers are available. A high accuracy locking mechanism is used to securely hold the condenser assembly in place, while still allowing for easy removal by a single lever.
Fluorescence
In fluorescent mode the Revolve uses a high sensitivity quantitative monochrome camera, which is wirelessly connected to the iPad display, providing a no-latency view when scanning a fluorescent plate or slide. High power discrete LED’s provide fluorescence excitation. Fluorescent wavelengths are specified by “light cube”, with a cube and filter block set provided for popular fluorescent excitation/emission spectra.
The user interface for fluorescence includes enough control to be useful, but avoids the excessive detail usually found on older imaging programs. You won’t have to worry about parallel shift voltage settings, or pre/post sensor clearing options just to snap an image! On-image display scaling, a simple high/low gain selection, and attenuation control are easily controlled. The physical knob on the right side of the microscope controls the current fluorescent channel in parallel with the app, providing a bidirectional link for the user’s preferred mode of operation.
Mechanical
The body includes a USB hub which can accept common memory sticks, allowing for quick USB transfer of images obtained by the iPad app. The engineers spent an extensive amount of time working on the question of “what do we do with the images on the iPad?”. This is an important question for every microscope, yet it never seems to be completely addressed. How many times have you realized images you captured simply were lost, because someone deleted them from your scope’s hard drive! With the Revolve you can save your images almost anywhere: USB, AirDrop, DropBox, with more cloud options coming soon. Or, just take your iPad….and walk away!
The focus mechanism is duplicated for easy access in either upright or inverted configuration, providing a common coarse/fine knob adjustment. X/Y adjustment is provided by dual knob control placed close to the user’s hand. The stage is locked into the microscope with a secure, but easily removable cam lock and alignment pins. This makes removal of the stage easy for revolving the scope, but keeps the stage securely in place when in use. Check out this video for an example of each of the above functions!
Conclusion
During my time working with the Echo Labs team, I’ve seen the attention to detail put into the user-focused features of this microscope. My previous posts have hopefully allowed a sense of understanding as to why I am so excited to work with this team! This company is a completely new approach to an old industry. The management team consists of veterans in the microscopy industry with a passion for high end imaging. The engineers are an amazing cadre with broad experience in the music, medical, defense, and research industries. Watching this team put the combined skill and experience into this microscope has been simply incredible. I hope you get a chance to experience using this microscope, as you’ll never look at scopes the same way again! Of course, in keeping with the idea of a new-generation company, you don’t need to talk with anyone just to check out pricing, an online and interactive quote configurator is available, which allows you to easily build the revolve for your work.
I believe Echo labs is well on the way to completely changing the microscopy industry. The Revolve is only the first step in bringing easy to use, fair price research instruments into the lab. Welcome to the Revolution.
Last month a friend gave me two old pairs of field glasses. One set was US Navy issue, which has the old-school build quality of a tank, and produces a bright, sharp image. The second pair was cheap and damaged. I’ve considered what to do with it for a while, and finally decided to tear it apart, and use the optical elements inside for educational, research and entertainment purposes. To that end I needed an adjustable optical platform, and while I have plans to make an optical table, for now I wanted to make a simple stack. Here’s how I did it.
Base with two optical elements attached
The base – I had an old aluminum base plate used on Sutter’s “LS” lamp series. We sometimes discard these bases during installs, so I managed to save this base from the scrap heap. I also snagged one of the support rods. This gave me a post with which to mount optics.
Next I needed something to hold the optics in place. I considered using band clamps, or other methods, but settled on making custom-cut holes that could accept the elements. If you want to do a similar project, you could use drill bits, a scroll saw, or even files to shape out the holes. I was itching to use my DIY CNC machine for something useful, so I employed it to cut the holes for me. I made a set of square blanks, and drilled a single alignment hole in each square. By using this hole as a center, I was able to make each different lens holder have a coaxial alignment, so that the lenses would stack up correctly.
Finished hole cut – note the alignment hole in the upper left side.
I’ve cut MDF (always wear a respirator when cutting MDF!) before, but have never had a good end mill for the job, so I finally made one by cutting one of my routing bits in half and sharpening the endpoints. The new bit chewed through the MDF with ease. To be extra careful I stepped my cuts at 0.050″ per route at a speed of 2ipm. This is a gentle/slow setup, but I wanted to make sure the parts came out well, and I didn’t want to push the machine for no reason. Finally, because I was cutting down nearly through the material, I set things up to leave a 0.010″ thick layer at the base of each cut. This way when the operation was done, I could simply push out the disk, and not risk cutting up my table on the machine. This process worked really well. Below is a video showing how easy it is to pop out the last layer.
With the holes all cut, I enlarged the alignment holes in each plate so that the plates would slip over the vertical rod I had. They fit snugly and allowed me to adjust the focus of each element as needed.
After spending a few minutes playing with the system I was able to set up optic trains providing magnification ranges from 10x to about 40x. The higher mag configurations didn’t look great, but here are some images I acquired using my iphone through the setup.
example configuration of lens elements
This was a fun project that only took about two hours to complete. Once I settle on an optimal configuration for these elements, I’ll post on it!
Believe it or not researchers at UC Berkeley found a way to make it happen. It uses a simple excitation diode and emission system, coupled to a cellphone’s camera.
