Category: Software

Analysis algorithms: performance quantification and ground truth

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 extracellular recording and open source software

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



iPad/iPhone/iOS app RayLab for optical design

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



ViRMEn – Virtual reality MATLAB engine

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 software for labs

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 open software for data exploration

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.



moco, fast open-source motion correction for 2-photon calcium imaging movies

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.



Open source structured illumination MATLAB 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



Ufora – easy parallel computing in Python

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.



CANDLE-J for denoising 2p data

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



Phase retrieval

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



Calcium imaging analysis GUI for MATLAB

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



CodeV, Zemax, OSLO, or …

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



PackIO for NI devices

Adam Packer wrote some LabVIEW software for acquiring and generating data from National Instruments cards called PackIO. It is meant to trigger and synchronize equipment as well as record any data, with a few specific modules for electrophysiology. The nice thing is that you can do just about everything in a hardware-timed fashion, so you’re



Voice control

Voice control has just recently become interesting to me. Ikuko bought me an Amazon Echo and I’m surprised at how useful I find it. I’m also surprised at how well it works– it can decipher my commands even when I’m whispering or mumbling from across the room. But the usefulness is what surprised me the