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guidance.sh
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git clone -b dev https://git.embl.de/oezdemir/OME_Zarr_Tools.git &&
source OME_Zarr_Tools/install.sh T0XMlxMdq8C6rSxurrdqMqHNrhyhC4f0 dRFXoR852egFtp3lC9NJPYjpPaCBNRa8
### Check what we have at our s3 bucket
mc tree s3minio/ome-zarr-course/
mc ls s3minio/ome-zarr-course/data/MFF/
mc ls s3minio/ome-zarr-course/data/JPEG/
### Convert the MFF data at the s3 end
batchconvert omezarr -st s3 -dt s3 --drop_series data/MFF data/ZARR/$USER;
### Convert the JPEGs by merging them to a single time series
batchconvert omezarr -st s3 -dt s3 --drop_series --merge_files --concatenation_order t data/JPEG data/ZARR/$USER;
### Check what has changed at the s3 end:
mc tree -d 2 s3minio/ome-zarr-course/
### Copy the Zarr data to the home folder
mc mirror s3minio/ome-zarr-course/data/ZARR/$USER ~/data/ZARR;
### Visualise locally and remotely with napari
napari --plugin napari-ome-zarr ~/data/ZARR/xyzct_8bit__mitosis.ome.zarr
napari --plugin napari-ome-zarr https://s3.embl.de/ome-zarr-course/data/ZARR/$USER/xyzct_8bit__mitosis.ome.zarr
### Visualise locally with fiji
fiji ;
### Other viewing options
https://kitware.github.io/itk-vtk-viewer/app/?fileToLoad=https://s3.embl.de/ome-zarr-course/data/ZARR/$USER/xyz_8bit__nucleus.ome.zarr
# add vizarr and neuroglancer
### REMOTE SEGMENTATION
# Have a look at the Zarr data before segmenting
mc tree -d 2 s3minio/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr
napari --plugin napari-ome-zarr https://s3.embl.de/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
# Segment both channels
zseg threshold -r -m otsu -c 1 -ch 0 -n otsu-c1-ch0 ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
zseg threshold -r -m otsu -c 1 -ch 1 -n otsu-c1-ch1 ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
# Have a look after segmenting
napari --plugin napari-ome-zarr https://s3.embl.de/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
# Postprocess via mathematical morphology
zseg postprocess -r -m binary_opening -f 1,1 -l otsu-c1-ch1 ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
#zseg postprocess -r -m binary_opening -f 2,2 -l otsu-c1-ch1 ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;
# Have a final look
mc tree -d 2 s3minio/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr
ome_zarr info mc tree -d 2 s3minio/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr
napari --plugin napari-ome-zarr https://s3.embl.de/ome-zarr-course/data/ZARR/$USER/23052022_D3_0002_positiveCTRL.ome.zarr;