Category: Software


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

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Optogenetics scattering iOS app

Here’s an iOS app which is basically a scattering calculator to help plan optogenetics experiments. There are also some plates from a brain atlas. (via the OpenOptogenetics blog)

Waterloo graphics for MATLAB

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.

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OpenSPIM and OpenSpinMicroscopy for light sheet microscopy

This month, Nature Methods highlights a couple of open light sheet microscopy projects. First up is OpenSPIM (pictured above). They have a nice web site set up here. They offer extensively detailed and clear directions for assembly. If Ikea sold a light sheet microscope, its directions would be opaque compared to this. The second one


GNOOM for spherical treadmill VR

Mice can learn to navigate virtual reality environments using a spherical treadmill, and this behavior drives place cell and grid cell activity. Christoph Schmidt-Hieber has started uploading his code to Google. GNOOM is a collection of virtual-reality tools for biomedical research. At the moment there’s only the optical mouse readout interface to Blender. But he’d

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Local cross corr images

One key step in analyzing data form calcium imaging experiments is segmentation (i.e., drawing regions of interest, ROIs). There have been some nice discussions in the literature (1, 2, 3, 4). Experiments with calcium dyes like OGB-1-AM, and those with genetically encoded indicators like GCaMP, require different approaches for drawing ROIs. Here’s some code I’ve

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MATLAB 2013a natively supports Kinect

There have been wrappers for interfacing with the Kinect device before, but the latest update to MATLAB makes it native to the Image Processing Toolbox. source Drop a Kinect in place of a video camera, and start getting 3D data for your experiments.


HG2 for Better Graphics in MATLAB

Undocumented MATLAB has an in depth look at the next generation graphics handler for MATLAB which you can use today, although it’s not officially released yet. Use the command line option “-hgVersion 2″ when launching MATLAB. See the post for more details.

Feedly, to replace Google Reader

Here’s a follow up on the previous post about alternatives to Google Reader (which is being shut down). Patrick Mineault commented that Feedly is looking good. I agree. Basic functionality is smooth and somewhat intuitive; layout and design are excellent.

Google Reader is going away

Google Reader is going to be shut down on July 1. If you use Reader, here’s what to do: Step 1: Export all of your subscriptions from Google Reader (takes less than 1 minute) Try these directions. It’s easy. Step 2: Start using an alternative, and import your old Google Reader stuff. (can take as

Python IDEs for science

xcorr has done a nice series of reviews of IDEs for scientific Python: First, Second, Third Previously Online scientific Python NEURON and Python

Commoditizing population calcium imaging analysis

More open source software to check out. Two-Photon Processor and SeNeCA – A freely available software package to process data from two-photon calcium imaging at speeds down to several ms per frame. Jakub Tomek, Ondrej Novak, and Josef Syka TJ Neurophysiol published 10 April 2013, 10.1152/jn.00087.2013 It’s notable in that it is an “all-in-one” package

Going back to Cali

No. I don’t think so. Anyways, CaliCode is a resource for population calcium imaging. It covers topics from inferring action potential trains from imaging data (hat tip to JV), to image processing and topical papers. P.S. If you get the reference, check out Game Rebellion’s version.

Electrophysiology software

Unenthusiastic about spending thousands of dollars on electrophysiology software like pCLAMP? Try the free and open source Strathclyde Electrophysiology Software. It’s a suite of programs for recording and analyzing signals from intracellular electrophysiology experiments. It’s for Windows. Many standard DAQs work right out of the box. Encouragingly, it has been updated routinely since 1997, including

Get the computation done

Programming that happens in labs is typically rushed and sloppy. The goal is to get the job done right, and, almost as important, done ASAP. The goal is not to generate ultra-readable, conforming code that is full-featured and ready for distribution. This is similar to the “Worse is Better” philosophy of software development (which I’ve