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dchaley / deepcell-imaging

Tools & guidance to scale DeepCell imaging on Google Cloud Batch
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Add script to enqueue QuPath job #312

Closed dchaley closed 3 weeks ago

dchaley commented 3 weeks ago

This script enqueues a Batch job to run QuPath measurements. It's intended to be the final step in a pipeline generating

(1) segmentation from DeepCell and (2) quantitative measurement reports from QuPath.

Fixes #311

Paired with @WeihaoGe1009

Example reports output:

Screenshot 2024-08-15 at 2 47 12 PM