Segmentation Scripts

Segmentation

This is an OMERO server-side script that uses Cellpose for cell segmentation.

segmentation.find_chan(image, channel)

Finds the specified channel number from the image metadata

segmentation.get_image_list(conn, parameter_map)

Gets image IDs from the list of images or dataset :param conn: The BlitzGateway :param parameter_map: The dataset’s id :return: image IDs or None

segmentation.run_script()

The main entry point of the script, as called by the client via the scripting service, passing the required parameters.

segmentation.segment_images(client, conn, image_ids, parameter_map)

Load images, segment cells using Cellpose, return masks as OMERO ROIs

Delete ROIs

This is an OMERO server-side script to perform bulk deletion of mask roi annotations.

delete_rois.delete_rois(conn, image_ids)

Delete all ROIs from an image

delete_rois.get_image_list(conn, parameter_map)

Gets image IDs from the list of images or dataset :param conn: The BlitzGateway :param parameter_map: The dataset’s id :return: image IDs or None

delete_rois.run_script()

The main entry point of the script, as called by the client via the scripting service, passing the required parameters.