Category: Software

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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 into regions of interest (ROIs) – extraction of dynamic signals from ROIs The included ROI Buddy software



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Scheme-it: online schematics integrated with Digikey

Scheme-it is an online electronics schematics/design tool that is integrated with Digikey’s catalog. This way, you can skip a step and go directly from design to order, without having to spend time sourcing parts. Handy.



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Cubehelix color scheme

Cubehelix is a color scheme that retains contrast as it is desaturated (top), as opposed to a more typical rainbow scheme (bottom). It’s great for look-up-tables (LUTs). Dave Green’s web site has multiple implementations of the color scheme, including code for R and MATLAB. More… Colorblind-proof color schemes Daltonization By the way, the If We



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OpenLabTools at Cambridge

OpenLabTools is a new initiative at Cambridge University, using engineering students to develop modular lab equipment. The OpenLabTools initiative aims to provide a forum and knowledge centre for the development of low cost and open access scientific tools, with an emphasis on undergraduate and graduate teaching and research. The programme is developed thanks to contributions



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FlyMAD

This tip comes from John Stowers. He and his colleagues developed an open source opto- and thermo- genetic system for targeting freely moving Drosophila with lasers. He wrote a long post discussing some of the technical challenges (Python, real-time considerations, architecture, distributing the software to colleagues, etc.) here. Thanks for sharing, John.



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3D Printing in Windows 8.1

Windows 8.1 has some interesting built-in support for 3D printing. They’re treating it a lot like 2D printing, even including a print preview. Labrigger still recommends outsourcing 3D printing because the technology is improving so fast. Shapeways, Ponoko, QuickParts and other places provide fast turnaround access to the best machines. That said, sometimes it’s nice



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OSX features I wish Windows had

Migrating back to Windows after years of using OSX, there are some features I miss. Default Folder X (link) Right click on the file name in the title bar to find out what folder that file came from. Rename a file that is already open. Click and drag events around on the native calendar app



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Meyer Navigator for ScanImage

Software from Stephan Meyer Zum Alten (Gilbert lab, Rockefeller): I put together a sort of Navigator for Janelia Farms ScanImage Two Photon control software, which we use a lot in our lab. There was no way in the existing version to visualize where you are, have been, distances, mark where you want to go back



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AutoHotKey for repetitive tasks

This the favorite tip Labrigger has received this week. Here it is, unedited, and in its entirety: I often use autohotkey for repetitive file naming and key remapping when I am forced to use clunky software on a windows computer I don’t plan on living on for long. It makes working with these programs much



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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,