Need help urgent

[Jonathan C. Henriksen]

Ali,

Take a look at QuPath and read through the docs. https://qupath.github.io/

It has built in tools to export tiles, included labeled image masks, for deep learning projects:
https://qupath.readthedocs.io/en/stable/docs/advanced/exporting_annotations.html?highlight=export%20tiles#binary-labeled-images

You will need to develop a script to convert the NDPI annotations into QuPath annotations. Search around on the active user forums, as someone may have already posted a similar question, e.g. https://forum.image.sc/t/importing-ndpa-annotation-files-into-qupath-code-attached/33721

Kind Regards,

Jonathan Henriksen
Laboratory Medicine and Pathology
Digital Pathology Coordinator for Anatomic Pathology
Research IT Coordinator for NWBioSpecimen Shared Resource
University of Washington
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