OpenMV is an open source machine vision system. It’s designed to be easy-to-use, with a gentle learning curve. They want this to be the “Arduino of Machine Vision”. The software IDE is free and open. The hardware is available from Sparkfun and other places. Color blob detection, eye and pupil tracking, motion detection, etc. You
I was cleaning house a bit, and among my old files I found this, which might be worth sharing. Years ago I made a centralized power supply for a custom 2-photon imaging system I built. There were two epi detectors (for red & green fluorescence) and three trans detectors (red, green, and IR-based “DIC-like Dodt”
We recently tweeted about a preprint from Eftychios A Pnevmatikakis and Andrea Giovannucci (code). The preprint is on motion correction for calcium imaging data. It is a nice quick read and discusses earlier work in the area. (That’s Eftychios of constrained-non-negative-matrix-factorization-for-calcium-imaging-analysis fame). Marius Pachitariu recognized the algorithm as very similar to one that he uses
SpikeGadgets makes hardware and software for extracellular array recording. They make nice looking hardware, both for recording from arrays, and for controlling experiments. They sell a few accessories as well, including this commutator. Their software is open source. MATLAB and Python code is also part of the project. The company’s run by Mattias Karlsson (worked
RayLab is an iOS app (iPhone/iPad) for optics analysis. It has some nice features– more than I expected. It’s a nice piece of work! For many practical applications it cannot replace conventional optic design software (e.g., Zemax/OSLO/CodeV). That said, it’s a very interesting product and worth checking out. It also does ACBD matrix analysis. Here
Dmitriy Aronov, while postdocing in David Tank’s lab at Princeton, developed a virtual reality engine that runs in MATLAB called ViRMEn. It’s open and there’s a good amount of documentation. The downloadable versions date back to 2013, and it is regularly updated. The most recent update as of the writing of this blog post was
Slack is very useful team coordination software. It’s been such a help in my own lab, that I suspect that given a properly configured Slack account, I could simultaneously run GE, Google, Intel, and the US Federal Government. It’s easy to dismiss Slack. To a large extent, it’s basically a bunch of chat rooms. I
Orange is a user friendly, graphical data mining package built with Python, from the University of Ljubljana. Check it out. They have a good blog for the project too.
Results are similar to the slow version of TurboReg, but it runs about twice as fast as the fast version of TurboReg. Here’s the paper. Here’s the code.
Peng Xi (Peking University) shared this resource his lab has developed: software for processing images for structured illumination (a superresolution technique). Here’s the Github repository. And here’s the paper (pay wall). Previously on Labrigger… Structured illumination Notes from an email exchange with the late Mats Gustafsson, a pioneer of structured illumination microscopy
It’s still early days, but this looks impressively good. Ufora might be one of the easiest-to-try ways to use parallel computing. With just a couple of lines of code, you can run your existing Python code on aws or another worker system.
Collaborative Approach for eNhanced Denoising under Low-light Excitation, or CANDLE, is a denoising algorithm specialized for the type of images that are acquired in 2-photon imaging applications. There’s code for both ImageJ and MATLAB available at that link. Here’s a write up on it. The raw images are on the left, and the denoised (via
Microscopists are often adapting techniques pioneered for astronomy. Adaptive optics is the example you all probably know. Relatedly, phase retrieval was originally developed for telescopic imaging systems, and was adapted for high NA microscopic imaging systems by Mats Gustafsson and colleagues (Hanser et al. 2003 Optics Letters). A couple of excellent optics people, Kyle Douglass
Stephan (currently in the Gilbert lab @ Rockefeller) wrote in to share his code for analyzing calcium signalling data in MATLAB. Thanks, Stephan! Stephan writes… I made a MATLAB GUI that automatically extracts ROIs from calcium imaging data. You can also add behavior data. Take a look if you feel like, try it out and
Trying to decide which optical design software to use? Just try them out and decide for yourself. I like how Steve Eckhardt (great guy, btw, in case you’re looking for someone to consult with) summarized their different strengths: “CodeV’s Global Synthesis is an extremely powerful global optimizer while Zemax makes it easy to take control
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