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. …
SIMA has recently been updated (here’s the original Labrigger post):
From the SIMA team:
We have recently released updated versions of the SIMA & ROI Buddy tools for analysis of calcium imaging data (motion correction, segmentation, registration…
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…
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…
Parula is the new default colormap for MATLAB (namesake above, actual map below). It probably collapses to grey better than jet (which is good for colorblind readers).
You aficionados care dearly about LUTs,…
(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…
Software Carpentry teaches scientists how to program and use open source tools to manage their data and make their life easier. They’re focussed specifically on software tools, rather than types of analysis, and so what…
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…
Nature Methods has a special on box plots, and in particular, the web app BoxPlotR.
Box plots are great. However, the conventions for box plots are not completely uniform (see below), and that can lead…
Infographic by Thomas Porostocky for WIRED.
Of course Labrigger emphatically supports the work of the Gates Foundation. However, we have to disagree with Bill Gates’ choice for Graph of the Year. Topic,…
Few things in biology take off like CRISPR genome engineering technology has recently. Feng Zhang’s lab at MIT…
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…
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…
