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dchaley / deepcell-imaging

Tools & guidance to scale DeepCell imaging on Google Cloud Batch
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Update QuPath job to run multiple predictions #301

Closed dchaley closed 1 month ago

dchaley commented 1 month ago

This updates the run-qupath-job batch job launcher to create a list of tasks, one for each pair of TIFF+npz files.

The tasks then run DeepCell and put the prediction mask TIFFs into the SEGMASK directory. This makes the dataset ready for QuPath processing.

Fixes #292.