Tag: micro-manager

  • ASCB 2015 Reveals the Next Generation of Microscopy

    One of the best aspects of flying is being apart from the world. Not only terra firma, but the troubles of life, questions of the future, and concerns of the present. Flight requires attention to instruments while in operation, but long cross country flights leave the pilot with time to sit and watch the world unfold beneath as time passes.

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    Departing from San Diego @ ASCB

    Night flight brings an even more isolated perspective, where after a few minutes alone, you watch the gauges, view the small points of light from far off cities, and feel suspended in the air, utterly alone in the earth.

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    Night Flight home in the cessna.

    So last night, flying home with the sun setting behind me, I had a chance to consider the past week of ASCB, and what it meant to me.

    Trade shows are hard. They are hard for the attendees and the exhibitioners. Attendees sit through lengthy talks, then browse the show floor and get bombarded by marketing, then have dinners with colleagues into the night. Exhibitors aren’t that different. Business meetings in the early morning, standing at the show floor booth all day, and then meetings and dinners with colleagues and contacts into the night. By the last day, everyone is happy to rest on the trip home!

    Yet somehow in this internet era, there’s nothing like meeting face to face, to share life, to discuss new projects, and meet new people. This year was my 14th year of attending trade shows as a member of the microscopy community. In that time things have changed in many ways, and are exactly the same in others. I hunted through the Blanco archives and found a few shots from my very first trade show. What an impression it made on me! This was from Neuroscience 2001, with my good friend Will Casavan. I was there working for Technical Instrument Company at the time, and Will was with Media Cybernetics. DSC00008

    Little did I know that it would be 14 years later, that Will would link me up with Echo labs, and a new and exciting chapter in my life would begin.

    I bring up the past for two reasons. First, because I enjoy looking back to see how far this industry has come. 14 years ago the hottest product on the market was the Nikon TE-2000, and it sported 2, yes 2!, cameras. One for fluorescence, and one for brightfield. The inverted microscope with cameras, computer, capture cards (yes, the cameras required a card, check out that data cable!), monitor, supporting electronic boxes and cables, took up a large bench worth of space, and ran about $65,000.

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    Noelle looking at a TE-2000 microscope equipped with fluorescence and brightfield cameras

    Some might argue that this industry hasn’t evolved quickly enough, but consider the following. Almost every function performed on the microscope above can also be performed using the ECHO Revolve. Of course, while at the booth I was able to airdrop images like this one straight to my phone, allowing me to easily post them on the blog!

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    Three channel fluorescence captured and airdropped to my iPhone in about 30 seconds using the Revolve microscope

    To me, this is a major step forward in research technology. I think the attendees who visited the ECHO booth would agree, as while working the booth I don’t think there was a single minute without at least 1 person looking at the scopes. In 2 of the 3 days I worked the booth, we couldn’t even break for lunch!

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    Yes, I was there, yes this is a selfie, don’t judge me 🙂

    While writing this, Eugene Cho, CEO of Echo labs, sent me a great timelapse of the show. I think this is an excellent video, as it shows the additional hard work required for exhibitors, to set up and tear down these displays. ECHO hand made the booth for the show, and the personal touch really made the booth stand out from the crowd in my opinion!

    Of course, there are many other advances taking place in the industry! I got to speak with Silvia Foppiano of Oko Lab, and was amazed how far incubation technology has come! In 2001, the best incubators I remember were homemade ones. Today, you can buy a stage top incubator, with magnetized connectors, micro-scale thermistor temp probes, humidity and co2 control, for prices around 1/3 of units in the past. As a machining junkie, I was very impressed with the finish of these units. If you are looking for an incubation solution you should definitely check them out.

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    Magnetized hold downs keep the chambered slide in place when being used with immersion oil
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    This little controller provides control and capture of all sensor data in the system.
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    Chamber has perfusion ports for dynamic experiments

    Zeiss has an awesome Oculus Rift-equipped demonstration of interactive sample observation. I couldn’t believe it when I walked by, there was the rift, and no-one was sitting in the demo chair! Boom 🙂 I had to jump on that chance. As a tech nerd and gaming junkie, I’ve been relishing the chance to test these, and it was a super cool experience! At first it’s disjointed to turn and see the image field move with the accelerometer inputs on the rift. Navigation was performed using an XBOX 360 controller.

    Zeiss ad for the Oculus Rift Cellular Visualization demo

    In only a few minutes I found my senses immersed in the environment, and was soon able to fly around with ease without even thinking about the control inputs required to do so. It really was like being in another environment. Excellent demonstration by Zeiss, and I’m happy to see that these types of technology are being adapted for use in biology.

    Sutter Instrument Company had the new IPA Integrated Patch Amplifier system on display at the show. This system is a huge leap forward for cell physiologists. With a single system, you get a matched probe, amplifier, and digital capture device, all optimized for low noise and maximum sensitivity. Definitely a major step for whole cell analysis!

    Sutters new IPA cell patch system

    Open-Imaging had a booth as well, demonstrating the new Micro-Manager 2.0 open source microscopy platform. IMG_6221

    I’ve seen a lot of new (read unstable) software at shows like this, and was surprised at how smoothly things worked. It’s obvious that Chris and Mark have put lots of time into this version, to make sure there’s minimal chaos factor when end users upgrade. I was also able to spend some time talking with Mark, as we flew to the show together this year! I’m excited for the future of Open Imaging, and am looking forward to working with the new release!

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    Mark Tsuchida takes the controls of a Mooney 201. We were speeding to the show at about 225MPH when I took this. Mark flew great!

    I want to give a special thanks to Sutter and Open Imaging, who both allowed me to present my Triggerscope at the show. I hope you got a chance to see it!

    My second observation is more a felt sense than a metric. Maybe it was the new product advancements, or my age, or who I spent tim with, but I felt a shift in generational control of the industry. During my early years in microscopy, there were a group of highly intelligent, capable and dedicated people who, in one form or another, directed the outcome of products and services in this industry. But now, a decade and a half has gone by, and I’ve realized that a new group of people are influencing that direction. While I may never get to place my personal mark on the industry, I know that I get to work near those who do.  To the people who led us here, I’d say thanks for working so hard to bring this industry such incredible capability. To those who now have the burden of keeping things new, I say bear this responsibly, not lightly. Our industry should be the hallmark of the highest ethical standards, have the strictest dedication to accuracy, and consistency. Our marketing should keep people captivated while only promising what we can deliver. We should price products fairly, and support them well. I hope we are up to the challenge, because it’s in our shoulders now.

    Yet…..when I did get a chance to walk the show floor this year, I took heart. I can see that the future is bright 🙂

    Austin

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    Sunset after the show, from the top of the SD convention center

     

  • Triggerscope & Micro-Manager Demo LED

    With ASCB right around the corner, I’ve been looking for opportunities to showcase the controller, so I’m happy and grateful to announce that the TriggerScope16 will be demonstrated at the Open-Imaging Micro-Manager booth (#1312)  this year!

    Here’s a short video I made showing the new display which will be at the booth. The display uses a NeopIxel (WS2812) strip, housed in a 1″ square extrusion, capped with a milled acrylic rod.

     

     

  • 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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