Years ago, Benjamin Judkewitz wanted to try some new techniques out with laser scanning two-photon microscopy. However, the software we were using was rather cumbersome to modify. So he wrote his own software from scratch…
This could be handy for some of you. Resonant scanners are fast, but inflexible. You can’t tell them where to go. They just oscillate at a fixed frequency. All you can do is control the…
The Thiele Lab at the University of Toronto is recruiting a Postdoc for the Fall to work with an HFSP team (UC Berkeley, Univ of Maryland, and Univ of Tübingen) that is investigating…
In this work, the authors used fast optical motion tracking and 2p imaging to measure the activity of individual neurons in freely moving animals. No surgery. No optical window. No restraint. And all the benefits…
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,…
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 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…
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…
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…
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.
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Bar-Noam et al. 2016 (Shy Shoham’s lab) figured out how to image the mouse retina with 2-photon microscopy in vivo.
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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…
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…
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…
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…