Lens designs
Posted in Hardware
In the talk I gave at the Short Course at SfN 2014, I briefly discussed the process of optical system design. A common strategy is to start with a published design, or at least a…
RStudio – MATLAB-like IDE for R
Posted in Software
Carson Chow recently shared his post-MATLAB suite of programming tools, and it involves RStudio, which is open-source. “I had planned to replace Matlab with Python, Julia, and R but I have…
Embrio for LabVIEW like programming of Arduino hardware
Embrio isn’t completely open. They want to sell $50 licenses. Let’s get that out of the way first. However, it is an interesting alternative for programming Arduino hardware. It’s a visual programming environment, like…
Cynicism on the frontier
Posted in Uncategorized
Excerpt from “How the Laser Happened: Adventures of a Scientist”:
We were still working under a Joint Service contract, managed by the U.S. Army Signal Corps. One day, after we had been at it…
Course in Paris
Posted in Uncategorized
The Optical Imaging and Electrophysiological Recording in Neuroscience course is Jun 9-19 in Paris. Application deadline is March 30. Lots of great people will be teaching, including Valentina Emiliani, Isabel Llano, Brad…
Remote, web-based analysis
Posted in Software
Jeremy Freeman and his lab are developing tools for analyzing data using a workflow that is fundamentally more scalable not only in terms of computing power and data set size, but also in collaboration and sharing. The one-person, one-machine approach to data analysis can be highly…
SLAB hiring postdocs
Posted in Tips
SLAB is hiring. See details at the link above (“Now Hiring!!“) or here: http://labrigger.com/blog/now-hiring/
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Sound dampening cabinets
Posted in Hardware
Experiment rooms can get noisy, so Labrigger puts the noisy bits in sound dampening cabinets like these. A separate room could be ideal, but this works too. Just put all the noisy equipment (rackmount portions…
FocusStack and StimServer for MATLAB
Posted in Software
Dylan Muir and Bjorn Kampa created some MATLAB code for two-photon calcium imaging experiments. First up is FocusStack, which provides a suite of analysis tools. Next up is StimServer, which coordinates visual stimulus generation and…
Photonics Handbook online reading
Posted in Tips
When you run out of catalogs to read, Photonics has some nice short articles. It’s all pretty basic, not too complicated. Good for training (e.g., Optical design software, Fiber lasers)
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SIMA update – for 2p calcium imaging
Posted in Software
SIMA has recently been updated (here’s the original Labrigger post):
From the SIMA team:
We have recently released updated versions of the SIMA & ROI Buddy tools for analysis of calcium imaging data (motion correction,…
NES – NeuroMat – browser-based data collection
Posted in Software
NES, from NeuroMat, is an open-source tool to manage clinical data gathered in hospitals and research institutions. Here’s their github link. More info from the lab.
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3D printed electronics
Posted in Hardware
It’s been promised for a while now, but someone has to do the hard work to make it happen. That inevitably involves some pretty pitiful looking stepping stones on the way to the…
Proper export for MATLAB figures
Posted in Software
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…