Andre and colleagues have a preprint up on their project generating inexpensive instrumentation for imaging and optogenetics experiments. The 100 Euro Lab: A 3-D Printable Open Source Platform For Fluorescence Microscopy, Optogenetics And Accurate Temperature Control During Behaviour Of Zebrafish, Drosophila And C. elegans. The authors use this instrumentation in courses at African universities. Open
Tag: calcium imaging
We recently tweeted about a preprint from Eftychios A Pnevmatikakis and Andrea Giovannucci (code). The preprint is on motion correction for calcium imaging data. It is a nice quick read and discusses earlier work in the area. (That’s Eftychios of constrained-non-negative-matrix-factorization-for-calcium-imaging-analysis fame). Marius Pachitariu recognized the algorithm as very similar to one that he uses
The Allen Institute has released the first set of data from their Brain Observatory project. Many of you already know about this, but I wanted to post about it to encourage people to take a bit of time to check out the data set themselves. They have a github page with materials that can help
The recent post on ripple noise generated some comments and additional discussion. Go check out the comments on that post. For example, Peter Rupprecht shared some snapshots an oscilloscope display showing the signal from the BNC connector at the back of the laser, in the presence of this ripple noise. The ripple is seen when
Andrew Lim wrote in to discuss strategies on dealing with ripple noise in 2-photon imaging systems, particularly when using resonant scanners. He writes: This isn’t so much a tip as a problem with resonant two-photon scopes that several people have told me they also have but I haven’t seen a solution for (other people apparently
Results are similar to the slow version of TurboReg, but it runs about twice as fast as the fast version of TurboReg. Here’s the paper. Here’s the code.
Bar-Noam et al. 2016 (Shy Shoham’s lab) figured out how to image the mouse retina with 2-photon microscopy in vivo.
I tweeted about this last fall. This is the best algorithm I’ve seen for segmenting and extracting time course from calcium imaging data. Eftychios Pnevmatikakis developed the code in Liam Paninski’s lab. The work is reported in a pair of papers in Neuron, and the code is freely available (links below). The source separation works
The UCLA Miniscope project is an NIH BRAIN Initiative-funded project to open source head-mounted calcium imaging devices. Their web site is online now. They’ll be releasing all of the information needed for making these devices yourself, including data analysis. They’ll also be holding workshops to train users. These devices compare favorably to commercial options. Inscopix
Compared to visible (vis) light, near infrared (NIR) wavelength scatters less and is less absorbed in brain tissue. If your fluorescent target absorbs vis light, then one way to use NIR is to flood the area with molecules that will absorb NIR and emit vis light. The process is called “upconversion“, since it is in
Stephan (currently in the Gilbert lab @ Rockefeller) wrote in to share his code for analyzing calcium signalling data in MATLAB. Thanks, Stephan! Stephan writes… I made a MATLAB GUI that automatically extracts ROIs from calcium imaging data. You can also add behavior data. Take a look if you feel like, try it out and
Following up SIMA, which has been covered here before: The SIMA team has released a new version of its toolbox that includes a spike inference algorithm developed by Eftychios Pnevmatikakis and Liam Paninski’s group. This approach permits the efficient estimation of the most likely spike train underlying a sequence of calcium imaging observations. The new
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 presentation. The paper is open access. In particular, Dylan’s MATLAB functions MappedTensor and TIFFStack are worth checking out. Both provide
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, segmentation, registration of ROIs across different imaging sessions, signal extraction). These new versions now support 3D datasets, allowing for analysis
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.
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