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

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

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

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

an hdf5/matlab file browser

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.

RStudio – MATLAB-like IDE for R

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 that R and Julia have been sufficient for my requirements.” It’s a nice environment and something to try if you’re looking for an

FocusStack and StimServer for MATLAB

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. The paper is open access. In particular, Dylan’s MATLAB functions MappedTensor and TIFFStack are worth checking out. Both provide

Proper export for MATLAB figures

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 project on Undocumented MATLAB.

Time-bandwidth product

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 bandwidth. Shorter pulses require wider bandwidths, and the product of pulse

Cubehelix color scheme

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 of the color scheme, including code for R and MATLAB. More… Colorblind-proof color schemes Daltonization By the way, the If We

ScanBox – free, open, MATLAB-based software for two-photon microscopy

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 up a blog and has several posts on it. Welcome to Scanbox Scanbox GUI Heart of Scanbox He also discusses


The BITalino is a microcontroller platform that comes with an array of sensors including sensors for electromyography (EMG), electrocardiography (ECG), electrodermal Activity (EDA), and more. They have several APIs, including Matlab, LabVIEW, Python, C#, and Java.

Visual stimulation and intrinsic imaging code

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 many neuroscience labs the world over. The implementation varies by lab, and Ian’s implementation is one that sees heavy use in the

Fast resonant scanning two-photon scope from UCLA

Here’s an update on the scope from Joshua Trachtenberg’s team. If you want one, contact them at: info.neurolabware@gmail.com This is another moving objective microscope, like the Sutter (Denk/MOM) scope, and the Thorlabs scope. Here’s a couple shots of objective rotation: Although it’s not shown in these images, the objective can be configured to move in

Waterloo graphics for MATLAB

Undocumented MATLAB has another post on improving graphics in MATLAB (previously). Waterloo is an easy-to-install package that generates nice graphics using Java. It can be used with MATLAB, R, and other software.