Tag: analysis

FocusStack and StimServer for MATLAB

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 update – for 2p calcium imaging

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,…



Proper export for MATLAB figures

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…



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…



What’s your favorite LUT?

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 …



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…



Software Carpentry teaching programming and data management to scientists

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…



StimFit

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…



Box plots vs. bar charts

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…



Is it really worth it to automate it?

We’ve been over this before.
Get the Computation Done.



Infographic by Thomas Porostocky for WIRED.

Bill Gates’ Graph of the Year

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….



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…



Plotly (plot.ly) 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,…



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 …



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…