Tools



Synapse Detection


Matlab scripts that use SVM to detect EPTA-stained synapses in electron microscopy images is available on Github. This is the custom analysis software used in Chandrasekaran S, Navlakha S, Audette NJ, McCreary DD, Suhan J, Bar-Joseph Z, and Barth AL. Unbiased, high-throughput electron microscopy analysis of experience-dependent synaptic changes in the neocortex. The Journal of Neuroscience, 16 Dec 2015, 35(50):16450-16462.

Cre Driver Full Brain Imaging


This is our in-house atlas of the cre driver lines we use. Endogenous eYFP fluorescence of 50 um brain sections of Ai3 animals crossed to somatostatin-, parvalbumin-, 5Htr3a-, and vasoactive intestinal peptide-cre (SS-cre, PV-cre, 5Ht-cre, VIP-cre) animals were imaged at 4x (NA=0.28), stitched with Fiji/ImageJ, and aligned with Adobe Photoshop. All animals were perfused with 4% PFA with picric acid.

SS-cre




PV-cre




5Ht-cre




VIP-cre




GIN


We also have an in-house atlas of GIN. GFP signal was enhanced by anti-GFP frozen section immunohistochemistry.



tdTomato