Optogenetics scattering iOS app
Posted in Software
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)
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Category: Software
Waterloo graphics for MATLAB
Posted in Software
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
Posted in Software
This month, Nature Methods highlights a couple of open light sheet microscopy projects.
First up…
GNOOM for spherical treadmill VR
Posted in Software
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. …
Local cross corr images
Posted in Software
One key step in analyzing data form calcium imaging experiments is segmentation (i.e., drawing regions of interest, ROIs). There have been…
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…
HG2 for Better Graphics in MATLAB
Posted in Software
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…
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…
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)
Python IDEs for science
Posted in Software
xcorr has done a nice series of reviews of IDEs for scientific Python: First, Second, Third
Previously
Online scientific Python
NEURON and Python
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Commoditizing population calcium imaging analysis
Posted in Software
More open source software to check out.
Two-Photon Processor and SeNeCA – A freely available software 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….
Electrophysiology software
Posted in 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….
Get the computation done
Posted in Software
Programming that happens in labs is typically rushed and sloppy. The goal is to get the job done right, and, almost as…
Make MATLAB text you
Posted in Software