Mrsic-Flogel Lab

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Protocols

This page relates to the paper "The logic of single-cell projections from visual cortex" by Han et al. (2018). Protocols relating to the fluorescence-based tracing can be found on our TissueVisionMods repository on GitHub. The releases page on that repository contains the latest PDF of the embedding protocol we use. Practical details for running the anatomy microscope along with modifications we made are on the repository wiki. We obtain point-spread functions on the TissueVision using ScanImage and we fit with measurePSF.

Code

Stitching of raw 2-photon tomography tiles and basic pre-processing were done using StitchIt. Visualising of the full-resolution data was done with MaSIV and cell tracing with MaSIV's neurite tracer plugin. Registration of the traced neurite trees to the Allen Atlas was conducted using ARA Tools, which just coordinates calls to Elastix via a MATLAB wrapper. The quality of the registration was assessed using Lasagna. Additional MATLAB tools for interacting with the Allen API are available from AllenBrainAPI. Code for analyses in the paper are at HanSingleCell (and related virus library data file).