Tag: python

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

Python ephys and calcium imaging analysis code

Andrew Giessel wrote some analysis code in Python when he worked in the Datta lab. He has since moved on to another venture, but he open-sourced the code. There are import routines for data from ScanImage and Ephus, but the majority of the code is acquisition platform agnostic. It’s called d_code.

SIMA – Image analysis from the Losonczy lab

(This post by the SIMA Team.) The SIMA (Sequential IMage Analysis) package facilitates analysis of time-series imaging data arising from fluorescence microscopy. The functionality of this package includes: – correction of motion artifacts – segmentation of imaging fields into regions of interest (ROIs) – extraction of dynamic signals from ROIs The included ROI Buddy software


This tip comes from John Stowers. He and his colleagues developed an open source opto- and thermo- genetic system for targeting freely moving Drosophila with lasers. He wrote a long post discussing some of the technical challenges (Python, real-time considerations, architecture, distributing the software to colleagues, etc.) here. Thanks for sharing, John.


Christoph Schmidt-Hieber and his collaborators Guzman and Schlogel have developed a cross platform (Linux, Windows, and OS X) application for analyzing electrophysiology data. Here’s the paper (open access). And here’s the code’s website. A key feature is that there’s a Python shell for scripting. Thus, in addition to being specialized software for analyzing electrophysiology data,


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.

Wakari Bundles – standardized Python for sharing code

I’ve been using Spyder recently for a MATLAB-like Python development environment (thanks for the tip, xcorr!). For python development within a browser window, I’ve used Wakari a bit. Now they have Bundles, which make it easier to share code with others because it takes care of all of the dependencies, and makes sure other people