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…
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…
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…
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…
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…
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…
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…
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…
Embrio isn’t completely open. They want to sell $50 licenses. Let’s get that out of the way first. However, it is an interesting alternative for programming Arduino hardware. It’s a visual programming environment, like…
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…
Dylan Muir and Bjorn Kampa created some MATLAB code for two-photon calcium imaging experiments. First up is FocusStack, which provides a suite of analysis tools. Next up is StimServer, which coordinates visual stimulus generation and…
SIMA has recently been updated (here’s the original Labrigger post):
From the SIMA team:
We have recently released updated versions of the SIMA & ROI Buddy tools for analysis of calcium imaging data (motion correction,…
NES, from NeuroMat, is an open-source tool to manage clinical data gathered in hospitals and research institutions. Here’s their github link. More info from the lab.
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Getting nice figures out of MATLAB can be a challenge. Sometimes it’s fine, but if you’ve hit upon a figure that simply isn’t exporting nicely (bad vector rendering, lost transparency, etc.), check out the…
