Years ago, Benjamin Judkewitz wanted to try some new techniques out with laser scanning two-photon microscopy. However, the software we were using was rather cumbersome to modify. So he wrote his own software from scratch…
This post is from Rob Campbell:
As part of TENSS we have created a set of examples showing how to use DAQmx in MATLAB without the Data Acquisition Toolbox. This is…
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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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 …
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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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…
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 presentation….
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 export_fig…
Ultrafast pulses are formed through interference of different wavelengths of light. Think of Fourier transforms, and how pulses can be generated through constructive and destructive interference of wavelengths with aligned phases. These wavelengths are close to the center wavelength, and spread over a wavelength…
Cubehelix is a color scheme that retains contrast as it is desaturated (top), as opposed to a more typical rainbow scheme (bottom). It’s great for look-up-tables (LUTs).
Dave Green’s web site has multiple implementations…
Dario Ringach has written some nice software for the Trachtenberg scope mentioned before on Labrigger. They also have put together their own Cypress PSoC-based hardware box to control several parts of the system.
He set…
Ian Nauhaus, whom UT Austin recently nabbed, is sharing his code for intrinsic imaging and visual stimulation.
The visual stimulation code is based off of Psychophysics Toolbox, which is already in use by…
