Open Sebastien-PILUSO opened 5 months ago
the deep-atlas-pipeline is producing an attached JSON file with the slice coordinates of whatever selected gene ID you want.
Can you point me to such a file?
and no documentation is provided in the main README.
The main README is quite large, but there is this: https://github.com/BlueBrain/atlas-densities/tree/main/atlas_densities/app/data/markers Which, I hope, covers the main points.
I think it would be good to move away from needing the fit_average_densities_ccfv2_config.json
file, as all the same configuration can be passed on the command line, and it makes these things more explicit.
I'm envisioning something like:
atlas-densities cell-densities fit-average-densities \
--hierarchy-path=data/1.json \
--annotation-path=data/ccfv2/annotation_25.nrrd \
--neuron-density-path=data/ccfv2/density_volumes/neuron_density.nrrd \
--average-densities-path=data/ccfv2/measurements/lit_densities.csv \
--homogenous-regions-path=data/ccfv2/measurements/homogeneous_regions.csv \
--marker=pv:868:PATH/TO/pvalb.nrrd \
--marker=sst:1001:PATH/TO/SST.nrrd \
--marker=vip:77371835:PATH/TO/VIP.nrrd \
--marker=gad67:479:PATH/TO/gad1.nrrd \
--realigned-slices=atlas_densities/app/data/markers/realigned_slices_ccfv2.json \
--cell-density-standard-deviations=atlas_densities/app/data/measurements/std_cells.json \
--fitted-densities-output-path=data/ccfv2/first_estimates/first_estimates.csv \
--fitting-maps-output-path=data/ccfv2/first_estimates/fitting.json
Can you point me to such a file?
Here is an example of the attached gene marker JSON file produced by the deep-atlas
pipeline for the coronal dataset id 479
corresponding to gad67
:
/gpfs/bbp.cscs.ch/data/project/proj84/piluso/deep-atlas2/processes_large/gene-to-nissl/ccfv2/479-metadata.json
I think it would be good to move away from needing the fit_average_densities_ccfv2_config.json file, as all the same configuration can be passed on the command line, and it makes these things more explicit.
Absolutely.
I'm envisioning something like:
Great this would be valuable.
I made the change here: https://github.com/BlueBrain/atlas-densities/pull/67 Can you try it @Sebastien-PILUSO / @lecriste to see if it's what you expected?
The new command looks good. I think @drodarie and @lecriste should also have a look at it. I will soon re-run the atlas densities staff, so we would see if it works well.
This does not change the behavior of the code, just how you pass parameters right? So you should not need my help / aproval on that one.
This does not change the behavior of the code, just how you pass parameters right?
That is correct, unless I have made a mistake.
The
fit_average_densities
command takes an indirect input which isrealigned_slices_ccfv2.json
viafit_average_densities_ccfv2_config.yaml
(see https://github.com/BlueBrain/atlas-densities/tree/main/atlas_densities/app/data/markers).However, this file (
realigned_slices_ccfv2.json
) embeds hard-coded slice coordinates in CCFv2 for manually chosen experiment IDs among the Allen ISH data portal for each used marker.First, this prevents any genericity in the input gene markers one user can give to the pipeline, where one must use these exact same data if we want the pipeline to work properly. Second, one
atlas-densities
user does not know such coordinates are used as it is hidden infit_average_densities_ccfv2_config.yaml
and no documentation is provided in the main README.This is at the junction between the
deep-atlas-pipeline
and theatlas-densities
pipeline. Actually, in addition to providing the realigned slices, thedeep-atlas-pipeline
is producing an attached JSON file with the slice coordinates of whatever selected gene ID you want.What I suggest:
realigned_slices_ccfv2.json
and add it at the beginning of thefit_average_densities
process,realigned_slices_ccfv2.json
as a direct input file to give to thefit_average_densities
command,