Category: Software

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Online app for comparing fluorescent proteins

George McNamara recently posted a comment on spectra, which referenced this online app which is handy.



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ImageSurfer 64-bit

UNC-Chapel Hill’s Computer Integrated Systems for Microscopy and Manipulation team released a new version of their popular ImageSurfer software. All 64-bit, with versions for Linux, OSX, and Windows.



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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 LUTs, as does Labrigger. Share your preferences in the comments. Do you prefer MATLAB’s jet colormap? ImageJ’s “Hot” LUTs (e.g., Green Hot, Cyan



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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