Adds Polygons around nuclei, works with image https://downloads.openmicroscopy.org/images/SVS/77928.svs Takes around 2 hours to run on that image, creating 160k polygons

nuclei_svs_segmentation.py

import omero
from omero.gateway import BlitzGateway
from omero.rtypes import rint, rstring

from skimage import morphology
from skimage import measure

# Adapted from https://gist.github.com/stefanv/7c296c26b0c3624746f4317bed6a3540

conn = BlitzGateway('user', 'password', port=4064, host='localhost')
conn.connect()
updateService = conn.getUpdateService()

image_id = 1257
image = conn.getObject("Image", image_id)
pixels = image.getPrimaryPixels()

size_x = image.getSizeX()
size_y = image.getSizeY()

start_x = 50000
start_y = 10000
cols = 40
rows = 45

tile_size = 1000

channel = 2
threshold = 14

def rgba_to_int(red, green, blue, alpha=255):
    """ Return the color as an Integer in RGBA encoding """
    r = red << 24
    g = green << 16
    b = blue << 8
    a = alpha
    rgba_int = r+g+b+a
    if (rgba_int > (2**31-1)):       # convert to signed 32-bit int
        rgba_int = rgba_int - 2**32
    return rgba_int

def add_polygon(contour, x_offset, y_offset):
    """ points is 2D list of [[x, y], [x, y]...]"""

    points = ["%s,%s" % (xy[1] + x_offset, xy[0] + y_offset) for xy in contour]
    points = ", ".join(points)

    polygon = omero.model.PolygonI()
    polygon.theZ = rint(0)
    polygon.theT = rint(0)
    polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
    # points = "10,20, 50,150, 200,200, 250,75"
    polygon.points = rstring(points)
    roi = omero.model.RoiI()
    # use the omero.model.ImageI that underlies the 'image' wrapper
    roi.setImage(image._obj)
    roi.addShape(polygon)
    # Save the ROI (saves any linked shapes too)
    updateService.saveObject(roi)

total = 0
tiles = 0
for col in range(cols):
    for row in range(rows):
        tiles += 1
        x = start_x + (col * tile_size)
        y = start_y + (row * tile_size)
        print('x, y', x, y)
        tile = pixels.getTile(theC=2, tile=(x, y, tile_size, tile_size))
        print(tile.shape)
        mask = tile < threshold
        mask = morphology.remove_small_objects(mask, min_size=10)
        mask = morphology.binary_dilation(mask)
        mask = morphology.binary_dilation(mask)
        mask = morphology.remove_small_holes(mask)
        contours = measure.find_contours(mask, 0)
        print('Found %s contours', len(contours))
        total += len(contours)
        print('total ROIS:', total, 'tiles', tiles)
        for c in contours:
            add_polygon(c, x, y)