Category: Software

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New algorithm for Open-SPIM

Labrigger talked about the Open-SPIM project last year. Since then, the project has proven to be vibrant and strong, with continuous improvements. Recently Stephan Preibisch came up with a multiview deconvolution algorithm (data pictured above) and the Open-SPIM project highlighted the work and its relevance to Open-SPIM.



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PubPeer browser plugins for PubMed

PubPeer has released browser plugins that add a line to PubMed results if there are comments on PubPeer for those publications. It looks like the example above. The install took less than 10 seconds. More on PubPeer



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ScanBox – free, open, MATLAB-based software for two-photon microscopy

Dario Ringach has written some nice software for the Trachtenberg scope mentioned before on Labrigger. They also have put together their own Cypress PSoC-based hardware box to control several parts of the system. He set up a blog and has several posts on it. Welcome to Scanbox Scanbox GUI Heart of Scanbox He also discusses



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Protocols.io – 3 days left

As Labrigger mentioned earlier this week, ZappyLab is running a Kickstarter campaign to jump start their crowd-sourced protocol repository, Protocols.io. Perhaps the most attractive reward they’re offering for pledging are the Black Russian Espresso cookies, made with vodka and Kahlua. The idea of Protocols.io is to mitigate the tendency for every lab to reinvent the



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ZappyLab Kickstarter: 1 week left!

This is exactly up the alley of what Labrigger is interested in supporting. There’s just one week left in their Kickstarter campaign. As of this writing, 300 people have contributed $30,000. With one final push this last week, they’ll meet their goal. They want to crowd source experimental protocols to increase efficiency and productivity. This



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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 website. A key feature is that there’s a Python shell for scripting. Thus, in addition to being specialized software for analyzing electrophysiology data,



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ACQ4: A Python-based open source system for neurophysiology

Luke Campagnola, Megan Kratz, and Paul Manis recently published their in-house software for neurophysiology experiments. It’s an extensive set of tools, including multiphoton imaging, photostimulation mapping, image mosaic construction, electrophysiology, and more. Website: acq4.org



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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 lead to confusion and make it take longer for a general audience to interpret the graphical representation of the data and



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Processing 2

One of the first posts in this blog was on Processing. Processing is a programming language with an integrated development environment that is specialized for simplicity– ease of learning and coding– and intended for applications that are primarily graphics-driven. Processing has seen continued development. Processing 2 is more OpenGL based, and for many applications, that’s



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Lazy Scholar Chrome plugin for searching for papers

Colby Vorland coded this Chrome plugin called Lazy Scholar to make it easier to find full text versions of papers. It basically cross references a bunch of databases for you, to find information on a particular paper you’re looking for. For example, in addition to trying to find a PDF for you, it also gives



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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.



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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, 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



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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:



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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