Category: Papers

Real-time tracking and 2p imaging with sub-ms timing

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 of multiphoton imaging. The project was undertaken by Marc Gershow and his lab, principally co-first authors Doycho Karagyozov and Mirna

Democratized state-of-the-art neuroscience

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

Pixy computer vision for tracking mouse behavior

Pixy is an open source computer vision system. Mostafa Nashaat, Robert Sachdev, and colleagues including Matthew Larkum have developed software for use with the Pixy, that can be used to track mouse behavior, including free movement around an enclosure (top image), or track the movement of individual whiskers (bottom image), all at 50 Hz. Here’s

DIY 1060 nm fiber laser

For less than $13,000, you can build your own fiber laser and get pretty nice images with it.

moco, fast open-source motion correction for 2-photon calcium imaging movies

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.

2-photon calcium imaging of the mouse retina in vivo

Bar-Noam et al. 2016 (Shy Shoham’s lab) figured out how to image the mouse retina with 2-photon microscopy in vivo.

Constrained non-negative matrix factorization for calcium imaging data analysis

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

New category of posts: papers

In the past, Labrigger has only rarely posted about relevant papers. That ends today. Now there’s a new post category for papers, and it’ll be used to highlight publications that are of potential interest to you, the community.