Example script for CellProfiler RunScript module

script.py

import cpscript
from scipy import ndimage

# either ask explicitely for an object
labels = cpscript.objects['Cells'].segmented
# or ask the user to choose one
# cpscript.objects.input_objects.require('The objects from which to measure the distance')
#labels = cpscript.objects.input_objects.segmented

background_labels = np.array(labels == 0, dtype=int)
dt_labels = ndimage.distance_transform_edt(background_labels)

# same with images etc.
imVSVG_pixels = cpscript.images['imVSVG'].pixel_data
# or again ask the user
# cpscript.images.input_image.require('The image to multiply with the distance transformed object-image')
# imVSVG_pixels = cpscript.images.input_image.pixel_data

imVSVG_dt_pixels = imVSVG_pixels * dt_labels
imVSVG_dr_pixels = imVSVG_pixels / dt_labels
imVSVG_dr_pixels[dt_labels == 0] = imVSVG_pixels[dt_labels == 0]

# output can also be provided in two ways
cpscript.images['imVSVG_dr_pixels'].pixel_data = imVSVG_dr_pixels
# here the user can name the output object within cellprofiler
# cpscript.images.output_image.provide('Name the output image')
# cpscript.images.output_image.pixel_data = imVSVG_dr_pixels