Another blog added
Posted in Software
Xcorr has some nice posts on coding, Plexon systems, analysis, and whatnot. It was just added to the Recommended Blogs section on the right. Some example posts:
A Plexon C++ API on 64-bit Linux…
Category: Software
Data’s killer app
Posted in Software
On the topic of the recent app post, I’ve been thinking about an old blog post from Peter Keane. The of his post is, “What is Data’s Killer App?” In it, he pondered the problem of data management.
After a not entirely apt analogy to HTML, Keane suggested that there is no killer app…
Apps
Posted in Software
You probably caught the article about the group who runs their laser-trapping experiments using an app they wrote for iOS on the iPad. This sparked a commentary about apps in science. What about some other apps for handheld and tablet computing?
Reference organization
In general, when it comes to…
More MATLAB code for 2p scope design
Posted in Software
In the last post, I mentioned how the “minification” factor (the diameter of the PMT detector divided by the diameter…
MATLAB code for designing collection optics for 2p scopes
Posted in Software
The Tsai book chapter from Ron Frostig’s CRC book is a great resource for building your own 2p microscope. In…
Labrigger Xmas Gift List 2010
Here’s the 2010 Labrigger Xmas Gift List.
Care to add anything?
Beam profiler
Measure the divergence of your laser beam, its stability, uniformity– all kinds of good stuff. These are useful metrics for diagnosing problems with the laser and really nailing the…
Igor Pro and Electrophysiology
Posted in Software
Igor Pro is a data analysis environment specialized for 1D time series data. It has some nice features: it handles data scaling beautifully, it has good…
Software for custom 2p scopes
Posted in Software
If you build your own two photon scope, you’ll need software. I mainly use the MATLAB-based ScanImage. Vijay Iyer (Janelia Farm) has really made it a slick, stable program. It cosmetically resembles…
Remote desktop software
Posted in Software
From time to time, you might catch me on my yacht, running an imaging experiment by remote desktopping into my rig from my laptop. I would use my iPhone, but I can’t fit all the windows for ScanImage onto the screen, even…
TIFFs in MATLAB
Posted in Software
MATLAB uses the open source library libtiff to write TIFF files, or they did the last time I asked. I work with multipage TIFFs a lot, and I find MATLAB is not…
Some OSX programs & tips
This is just a quick post to highlight a few Mac OSX programs & tips that you might find useful.
Programs
Default Folder – This is how all save file dialogs should work. Watch…
Colorblind-proof two color scheme
Posted in Software
The usual color scheme for showing co-localization is to overlay a red image and a green image and have the yellow portions show the sites of co-localization. This is problematic since red-green colorblind…
TREES: MATLAB toolbox
Posted in Software
A new paper in PLoS Computation Biology proposes an elegant formalism for describing neuronal morphology. The reason I’m highlighting it on Labrigger is because the authors have simultaneously released a very extensive,…
Processing
Posted in Software
Processing is a programming language geared towards visual artists, but it comes in handy for a lot of other purposes as well. Here are some of its finer points:
Open source
Integrated IDE (see…
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