detect_rois_omero

Set of helper functions for automatically generating bounding boxes for OMERO slidescans

Functions

Session creation

• create_json_session(web_host, username, password): creates a session/CSRF token for usage with the JSON OMERO API.
• create_blitz_session(host, username, password): creates and connects a BlitzGateway object with a session for usage with the Blitz OMERO API.

Image retrieval

• retrieve_image(session, base_url, image_id, scaling_factor): retrieves a jpeg for a 2D image from OMERO (given an image ID), scaled down by a scaling factor. session and base_url are outputs from create_json_session. Output is a 2D+RGB numpy array.
• get_image(conn, image_id): retrieves an Image object from OMERO (given an image ID), using the Blitz API, from the BlitzGateway object specified by conn.

ROI generation

• create_rois(image, minimum_size, method, closing, scale_factor): creates ordered (left/right/top/bottom) ROIs that should approximate each slice in a slide scan. Uses thresholding based on a specified method (from 'triangle', 'otsu', 'yen', 'li'), filters by a minimum specified size in "full-resolution" pixels (i.e. the minimum size in pixels of ROI in the full-res image), morphologically closes regions using a specified closing radius and then creates, merges appropriately and orders ROIs.

ROI uploading

• save_rois(image, regions, scaling_factor, rerun): saves ROIs back to OMERO - needs to use the Blitz API due to ROI saving not being supported via JSON API, and therefore needs an Image object retrieved from OMERO via Blitz API. Scaling factor needs to be specified here to scale ROIs back to full-size image server-side. Added a "--rerun" option for running the same code multiple times over the same image - it deletes ALL existing ROIs on that image before saving the new ones.

Example usage

    from create_session import create_json_session, create_blitz_session
    from retrieve_image import retrieve_image, get_image
    from save_rois import save_rois
    from create_rois import create_rois

    login_rsp, session, base_url = create_json_session(WEB_HOSTNAME, USERNAME, PASSWORD)
    img = retrieve_image(session, base_url, img_id, scale_factor)
    regions = create_rois(img, min_size, method, closing)
    conn = create_blitz_session(HOSTNAME, USERNAME, PASSWORD)
    image = get_image(conn, img_id)
    save_rois(image, regions, scale_factor)
    conn.close()