histomicstk.workflows.specific_workflows

Created on Tue Oct 1 01:38:16 2019.

@author: mtageld

histomicstk.workflows.specific_workflows.cellularity_detection_workflow(gc, cdo, slide_id, monitorPrefix='', destination_folder_id=None, keep_existing_annotations=False)[source]

Run cellularity detection for single slide.

The cellularity detection algorithm can either be Cellularity_detector_superpixels or Cellularity_detector_thresholding.

Parameters
  • gc (object) – girder client object

  • cdo (object) – Cellularity_detector object instance. Can either be Cellularity_detector_superpixels() or Cellularity_detector_thresholding(). The thresholding-based workflow seems to be more robust, despite being simpler.

  • slide_id (str) – girder id of slide on which workflow is done

  • monitorPrefix (str) – this will set the cds monitorPrefix attribute

  • destination_folder_id (str or None) – if not None, copy slide to this girder folder and post results there instead of original slide.

  • keep_existing_annotations (bool) – keep existing annotations in slide when posting results?