plexora dataset create
Make a dataset, registering its images if needed.
Usage
plexora dataset create [-h] [--images PATH [PATH ...]] [--from SPEC.json]
[--scan DIR [DIR ...]] [--dry-run] [--description DESCRIPTION]
[--node NAME] [--exist-ok] [--json]
nameArguments
namerequiredOptions
--images PATH [PATH ...]Images to register as projects and put in it. An image is all a project needs.
--from SPEC.jsonA JSON file: {name, description, projects: [...]} or a bare list of project specs. Command-line arguments win over what is in it.
--scan DIR [DIR ...]Folders to scan. Every image under them becomes a project, with the segmentation mask, cell table and channel names matched to it by name and folder. Files that cannot be matched with confidence are listed and left out. With --node, folders on that data node.
--dry-runWith --scan: show what would be created and register nothing. With --json, print it as a spec file that --from reads, to edit and rerun.
--description DESCRIPTION--node NAMEThe data node these files are on. Every path that does not say otherwise is a path over there, and the projects address it rather than copying anything here.
--exist-okAdd to the dataset if it already exists.
--jsonPrint the result as JSON.
Examples
Register images as projects and group them
plexora dataset create "Melanoma cohort" --images slide1.ome.tif slide2.ome.tif --description "Stage III, 2024"From a JSON spec of several projects
plexora dataset create "Melanoma cohort" --from cohort.jsonFiles that live on a data node
plexora dataset create "Cluster cohort" --node hpc --images /scratch/me/slide1.ome.tif /scratch/me/slide2.ome.tifScan a folder and show what would be created
plexora dataset create "Melanoma cohort" --scan /data/cohort --dry-runPrint the scan as a spec file that --from reads, to save and edit
plexora dataset create "Melanoma cohort" --scan /data/cohort --dry-run --jsonPython equivalent
import plexora
cohort = plexora.create_dataset(
"Melanoma cohort",
images=["slide1.ome.tif", "slide2.ome.tif"],
description="Stage III, 2024",
)