retune-commons / bart

#TESTMODE# Atlas registration to single histological slice (warps atlas onto slice, cell counting, calculation of cell density for observed region)

🚀 # TEST-MODE ...the current REPO does not WORK!!!

BART

Register the Allen Mouse atlas to single histological slice (warps atlas onto slice, cell counting, calculation of cell density for observed region).

UPDATES

🔵 Inspect last changes/updates.

TEMPLATE

• Allen Mouse template can be downloaded from: https://drive.google.com/drive/u/0/folders/1Bod4JqHYkzvGnBS465xfOti2OF89_lL9

Installation

Installation via GITHUB using GIT

ADVANTAGE: updates can be made via toolbox

• download & install GIT client --> https://git-scm.com/downloads just follow instructions and keep the default properties
• browse to LINK: https://github.com/ChariteExpMri/bart
• select "install_bart.m" and click [RAW]-button or go to here: https://raw.githubusercontent.com/ChariteExpMri/bart/master/install_bart.m
• select "save as" (cmd+s or ctrl+s) and save file as "install_bart.m"
• copy "install_bart.m" to the location where bart should be installed. ..please don't create a folder with name "bart", this folder will be created later on

OPEN GUI

• set MATLAB's current working dir to the location of "bart"
• type 'bart'

-download "install_bart.m". -save "install_bart.m" at the location where bart should be installed. -in matlab run "install_bart.m"

IMPORTANT

xx https://ui.toast.com/tui-editor