SPT
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nadeemlab
Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images (https://oncopathtk.org)
The ondemand containers (counts service, squidpy metrics service, etc.) currently load up their in-memory data stores on initialization. It takes about 5 minutes for our current list of ~6 datasets....
For better flexibility on the frontend side, let's make the API handlers support lower-cased normalized versions of the study names throughout. This is probably as simple as updating the `_retrieve_study_database`...
When the cell-data API endpoint is queried for a sample with a large number of cells (e.g. 700k), the query seems to be forwarded correctly to the cells service, which...
- [ ] Support ADI/SpatialData (https://github.com/scverse/spatialdata) conversion. - [ ] Submit SPT for inclusion in the scverse ecosystem (see requirements here: https://github.com/scverse/ecosystem-packages).
In some cases a pending metric that raises a ValueError fails to end the job and wrap up. This causes infinitely pending metric calculation. ```txt ondemand | 03-18 23:26:49 [...
We also discussed how the `[upload-importance]` section in a graph config file should be generated instead of manually written by the user, at least in Nextflow workflow, since the plugin...
Current default behavior is to use the `latest` image tag for the SPT docker image in Singularity and Docker Nextflow workflows, but we observed an issue where Singularity doesn't check...
Since we're adapting pathology datasets for use in machine learning, often our datasets end up being imbalanced, e.g., the treatment non-responding set ends up having 2x the number of graphs...
I often find myself editing the `workflow` Makefiles when I'm investigating issues with `spt workflow configure` and `nextflow run` so I can see what's wrong with the processes being run...
The full test suite now takes about 8 minutes, which is long enough to significantly slow down development. Moreover, despite the "unit test" and "module test" labels, most of the...