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 project on Undocumented MATLAB.
Ultrafast pulses are formed through interference of different wavelengths of light. Think of Fourier transforms, and how pulses can be generated through constructive and destructive interference of wavelengths with aligned phases. These wavelengths are close to the center wavelength, and spread over a wavelength bandwidth. Shorter pulses require wider bandwidths, and the product of pulse
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 and Ephus, but the majority of the code is acquisition platform agnostic. It’s called d_code.
George McNamara recently posted a comment on spectra, which referenced this online app which is handy.
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.
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
(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
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.
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
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
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.
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
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
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
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
- Cheap DIY Kwik-Cast on
- Constrained non-negative matrix factorization for calcium imaging data analysis on
- Test slides on
- Test slides on
- miniPCR – $500 diy open thermocycler on
- SciScan: Scientifica’s two photon software on
- Numberfactory: extremely useful reference on
- NEURON + Python in OSX on
- Coolant lines for lasers on
- Coolant lines for lasers on
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