idr0173-breiter-alphasynuclein

Import

Install mamba:

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

source ~/.bashrc

micromamba create -n import -c conda-forge -c ome omero-py

micromamba activate import

# Install omero-cli-zarr (TODO: replace with release/RC)
git clone https://github.com/ome/omero-cli-zarr.git
cd omero-cli-zarr
pip install -e .

Setup Project:

omero login
omero obj new Project name="idr0173-breiter-alphasynuclein/experimentA"
/uod/idr/metadata/idr-utils/scripts/create_datasets.sh [ID!] idr0173-experimentA-filePaths.tsv > /tmp/173_dataset.out
grep ", Dataset:" /tmp/173_dataset.out | sed "s/.\+,//g" > /tmp/173_dataset.ids

parallel -j 4 --eta --progress --colsep '\t' --delay 1 -k --joblog /tmp/173.log omero zarr import --target-by-name {1} --name {3} {2} :::: idr0173-experimentA-filePaths.tsv

Then (important to do before browsing the dataset!):

parallel -j 4 --eta --progress --delay 3 omero render test --thumb :::: /tmp/173_dataset.ids

Rois

 pip install pandas omero-rois
 cd scripts
 python rois.py