Google Reader is going to be shut down on July 1. If you use Reader, here’s what to do: Step 1: Export all of your subscriptions from Google Reader (takes less than 1 minute) Try these directions. It’s easy. Step 2: Start using an alternative, and import your old Google Reader stuff. (can take as
xcorr has done a nice series of reviews of IDEs for scientific Python: First, Second, Third Previously Online scientific Python NEURON and Python
More open source software to check out. Two-Photon Processor and SeNeCA – A freely available software package to process data from two-photon calcium imaging at speeds down to several ms per frame. Jakub Tomek, Ondrej Novak, and Josef Syka TJ Neurophysiol published 10 April 2013, 10.1152/jn.00087.2013 It’s notable in that it is an “all-in-one” package
No. I don’t think so. Anyways, CaliCode is a resource for population calcium imaging. It covers topics from inferring action potential trains from imaging data (hat tip to JV), to image processing and topical papers. P.S. If you get the reference, check out Game Rebellion’s version.
Unenthusiastic about spending thousands of dollars on electrophysiology software like pCLAMP? Try the free and open source Strathclyde Electrophysiology Software. It’s a suite of programs for recording and analyzing signals from intracellular electrophysiology experiments. It’s for Windows. Many standard DAQs work right out of the box. Encouragingly, it has been updated routinely since 1997, including
Programming that happens in labs is typically rushed and sloppy. The goal is to get the job done right, and, almost as important, done ASAP. The goal is not to generate ultra-readable, conforming code that is full-featured and ready for distribution. This is similar to the “Worse is Better” philosophy of software development (which I’ve
Patrick Mineault covered this back in November in his always interesting xcorr blog. Using some small code snippets, you can set up MATLAB to text you when, say, it’s done with a long data processing script or model run. (link)
If you like Python, want to analyze data online, and are interested in a standardized environment that can be easily shared, read on: Continuum Analytics is offering a new beta: Wakari. You can register to try it out! If you’re an academic frustrated by setting up computing environments and annoyed that your colleagues can’t easily
Post publication peer review has yet to really take off, but Labrigger hopes it does. One of the newest sites is PubPeer. PubPeer does it right, allowing for anonymity. This is important in order to obtain candid opinions from the scientific community. The bland and boring reviews at F1000 show what comes out when anonymity
Sometimes it’s possible to use aftermarket software (or firmware) to make consumer products function for lab applications. In this post, I’ll cover some software for iOS cameras and Canon cameras that add functions useful for scientific applications. There are a bunch of apps for iOS devices with cameras that add some useful features. An app
Last Monday, Labrigger covered HelioScan, a LabVIEW-based, two-photon laser scanning microscopy software suite. Marcel van ‘t Hoff (left) and Dominik Langer (right) are the two main developers of HelioScan. They were kind enough to answer some interview questions for Labrigger. LR: Are there special considerations you had to make when designing HelioScan? What measures did
HelioScan is a LabVIEW-based software suite from Fritjof Helmchen’s group that is specialized for running 2 photon microscopes, and is carefully designed to be modular. This modularity is intended to make it more easily adapted for different rigs and experiments, and robust to the frequent version forking that happens in lab environments. It’s all open
LabVIEW is a great tool, but the block diagrams can become a mess if the programmer isn’t careful. This book was recommended to me by David Ferster, whose LabVIEW code is very clean and eloquent, and I wanted to pass the tip onto the Labrigger audience.
UPDATED! This question has come up a number of times recently: how does one get NEURON to run with Python support on OS X. At this time, there’s no simple way to install NEURON with Python support any more because Eilif’s package is outdated and won’t run with current EPD and XCode versions. The only
Micro-Manager (µ-Manager) is an open, ImageJ-based suite of code for controlling microscopes and associated instrumentation. Check out the list of supported equipment.
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