Commit 3b2699a9 authored by Romain Guiet's avatar Romain Guiet
Browse files

readme with some instructions

parent 2a9e123f
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# DATA :
## from terminal :
### to see large file available
git lfs ls-files
###to download them
git lfs pull
# download and unzip
wget https://zenodo.org/record/5018719/files/MouseBrainCoronalSerialSections.zip image.zip && 7z x image.zip
# To unzip serial-coronal-sections dataset use p7zip via the command > 7z x Mouse....zip
# Software install
## In Fiji :
- set elastix and transformix path :
- Plugins > BIOP > Set and Check Wrappers
- /opt/elastix-5.0.1-linux/bin/elastix
- /opt/elastix-5.0.1-linux/bin/transfromix
-abba bdv , specify path to :
-brain map : file:/home/jovyan/work/abba-biop-vm/data/allen-mouse-ccf-v3-labels-modulo-65000/ccf2017-mod65000-border-centered-mm-bc.xml
-brain ontology : file:/home/jovyan/work/abba-biop-vm/data/allen-mouse-ccf-v3-labels-modulo-65000/1.json
## In QuPath :
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