GitHub - LehtinenLab/Shipley2020: Code used Shipley et al. (2020), Neuron (original) (raw)

Code for Shipley, Dani et al. (2020)

This repository contains all of the code necessary for XYZT registration and segmentation of ChP blood vessel images.

/data

This folder contains supporting code necessary for loading tiffs, writing .sbx (binary) files, writing metadata, and various other support programs.

/registration

This folder contains the code used in the various steps of registration. To get started, run RegistrationMasterPipeine.m, and edit the first block of code to point to your data.

/vessel segmentation

This folder has the code necessary for segmenting PECAM-stained images, dilating the periluminal space, and comparing manually segmented images to automatically segmented images.