Cloud storage is not the cure-all it is sometimes proposed to be. On-campus servers have some advantages in transmission speed and cost, especially as storage requirements grow considerably. Talk to your campus IT services before shelling…
Pixy is an open source computer vision system. Mostafa Nashaat, Robert Sachdev, and colleagues including Matthew Larkum have developed software for use with the Pixy, that can be used to track mouse behavior, including free movement around…
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…
SpikeGadgets makes hardware and software for extracellular array recording.
They make nice looking hardware, both for recording from arrays, and for controlling experiments.
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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.
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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.
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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…
I tweeted about this last fall. This is the best algorithm I’ve seen for segmenting and extracting time course from calcium imaging data. Eftychios Pnevmatikakis developed the code in Liam Paninski’s lab. The…
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…
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…
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…
Michael Graupner has coded a nice program for browsing and managing hdf5 files (closely related to MATLAB files) called hdf5Manager. And it’s open source.
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Following up SIMA, which has been covered here before:
The SIMA team has released a new version of its toolbox that includes a spike inference algorithm developed by Eftychios Pnevmatikakis and Liam Paninski’s group….
Carson Chow recently shared his post-MATLAB suite of programming tools, and it involves RStudio, which is open-source. “I had planned to replace Matlab with Python, Julia, and R but I have found…
Jeremy Freeman and his lab are developing tools for analyzing data using a workflow that is fundamentally more scalable not only in terms of computing power and data set size, but also in collaboration and sharing. The one-person, one-machine approach to data analysis can be highly…