pipex_batch_list_EXAMPLE.txt

#my ubuntu laptop needs 8GB more of RAM to handle the images

swap 8

#running ESPACE experiment 3

segmentation.py -data=/home/lab/pipeline/data -nuclei_marker=DAPI -nuclei_diameter=20 -nuclei_expansion=20 -membrane_marker=CDH1 -membrane_diameter=25 -measure_markers=DAPI,CDH1,HLA-DR,CHGA,KRT5,IAPP,ACTA2,GORASP2,EZR,SST,TUFM,S100B,HSP90B1,Ki67,RBP4,AMY2A,NEFM,Panck,HLA-DR,GCG

analysis.py -data=/home/lab/pipeline/data -analysis_markers=HLA-DR,CHGA,KRT5,IAPP,ACTA2,RBP4,AMY2A,NEFM,Panck,HLA-DR,GCG -image_size=2000 -leiden=yes

#need full TissUUmaps integration, with cluster

generate_geojson.py -data=/home/lab/pipeline/data -expand=yes

generate_tissuumaps.py -data=/home/lab/pipeline/data -include_marker_images=DAPI,CDH1,HLA-DR,CHGA,KRT5 -include_geojson=yes -compress_geojson=yes -include_html=yes