split probability_map.csv into isocortex layers #49
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* instead of using probability_map.csv, one can create the nrrd files
split by layer:
atlas-densities mtype-densities create-from-probability-map \
--synapse-class INH \
--hierarchy-path=../data/1.json \
--annotation-path=../data/ccfv2/annotation_25.nrrd \
--probability-map $BASE/L1_probability_map.csv \
--probability-map $BASE/L23_probability_map.csv \
--probability-map $BASE/L4_probability_map.csv \
--probability-map $BASE/L5_probability_map.csv \
--probability-map $BASE/L6_probability_map.csv \
--marker gad67 $MOL/gad67.nrrd \
--marker pv $MOL/pv.nrrd \
--marker sst $MOL/sst.nrrd \
--marker vip $MOL/vip.nrrd \
--marker approx_lamp5 $MOL/approx_lamp5.nrrd \
--output-dir=output
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #49 +/- ##
=======================================
Coverage ? 97.76%
=======================================
Files ? 22
Lines ? 1385
Branches ? 0
=======================================
Hits ? 1354
Misses ? 31
Partials ? 0
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
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This was meant to show that the split layers probabilities worked; not to be merged - closing. |
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atlas-densities mtype-densities create-from-probability-map
--synapse-class INH
--hierarchy-path=../data/1.json
--annotation-path=../data/ccfv2/annotation_25.nrrd
--probability-map $BASE/L1_probability_map.csv
--probability-map $BASE/L23_probability_map.csv
--probability-map $BASE/L4_probability_map.csv
--probability-map $BASE/L5_probability_map.csv
--probability-map $BASE/L6_probability_map.csv
--marker gad67 $MOL/gad67.nrrd
--marker pv $MOL/pv.nrrd
--marker sst $MOL/sst.nrrd
--marker vip $MOL/vip.nrrd
--marker approx_lamp5 $MOL/approx_lamp5.nrrd
--output-dir=output