Tag: microscope automation

  • On a lifetime of Learning

    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

    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?
    This kickstarter campaign will provide classes on AI using openCV. https://www.learnopencv.com/

    Step 3: Take the next class

    A drone you can make on your own is described by Nathan Vertile here

    Step 4: The finals Exam

    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.

    -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

     

     

     

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