Closed dchaley closed 2 months ago
Note that we need the segmentation to produce a tiff for the whole-cell mask, and for the nucleus mask. I don't know if we even output correctly with compartment=both
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RESULT: we don't, #298
The target environment doesn't have the Batch job dependency preview enabled.
We'll need an alternate approach. One idea: add another task runnable. All TASK_INDEX except 0 immediately stop. The zero'th task simply submits the next job: QuPath measurements.
New dependency: the runnable mentioned above. #311
Once we have that runnable, this ticket becomes: add it as the last task.
Update: #315 added the job, but along the way measurement broke– will close this on fix.
We did it 🏆
scripts/segment-and-measure.py
Create a job launcher that works on a QuPath dataset root, which submits a job:
292: Segment the NPZ files present in the project. ← this is the DeepCell container
311: On completion, enqueue the QuPath measurement job.
The QuPath measurement job:
293: Create the QuPath project & output measurement reports.
Note that we use the final runnable because the Job Dependencies preview isn't available in the target environment.