Create QuPath segment + measure job

[dchaley]

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.

[dchaley]

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.

RESULT: we don't, #298

[dchaley]

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.

[dchaley]

New dependency: the runnable mentioned above. #311

Once we have that runnable, this ticket becomes: add it as the last task.

[dchaley]

Update: #315 added the job, but along the way measurement broke– will close this on fix.

[dchaley]

We did it 🏆

scripts/segment-and-measure.py