Category: Software


CRISPR resources from the Zhang Lab at MIT

Few things in biology take off like CRISPR genome engineering technology has recently. Feng Zhang’s lab at MIT has a design tool for CRISPR that has also rapidly matured. It helps to avoid off target effects.


Plotly ( for collaborative data visualization and analysis

It could be described as a GoogleDocs-type app for data analysis. But that would be a lazy description. Import your data, code up the analysis and visualization, and then share with collaborators who can view, modify, and contribute. They have APIs for Python, MATLAB, R, Julia, Perl, Ruby, and Arduino (import directly from hardware– example

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SciScan: Scientifica’s two photon software

My friend Bruno has written some very nice software for Scientifica’s two photon microscope systems. It’s called SciScan. It’s written in LabVIEW and runs both their conventional galvo and resonant systems. These screenshots are all from the conventional galvo version of the software, but the resonant version looks almost identical (there’s no arbitrary line scan


Sharing your code

Someone recently asked me, “What’s a good way I can share my code?” There are several ways you can go, of course. Here are the first two that popped into my mind. A full web site Squarespace isn’t a bad option. The designs are good. The option called Flatiron is what’s used for this site:


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

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Helioscan paper is out

The Helioscan paper is out now in J Neurosci Methods. Mentioned previously on Labrigger. Here’s a Labrigger interview with the developers.


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.