Feeding CellProfiler Manually Segmented Images




Is there any way to manually segment cells in black and white, i.e drawing the outlines using Fiji, and then feed that into CellProfiler and have it accurately identify the objects? There seems to be no option for passing in already segmented cells without it being a segmentation mask with different colors per outline.



Hi Sabrina,

CellProfiler only takes masks, not outlines, as you described, but there are two options

  1. Draw the outlines instead of in FIJI in our IdentifyObjectsManually module; as a bonus, you can save the object image after identification so if you do decide to do a different analysis later, you only have to draw the outlines once

  2. You can try to follow this tutorial; it’s a bit experimental but may work!