Cropping Variable Well Plate Images

Hello!

I am trying to find an automated method of automatically cropping the exterior of a well from the ROI (see example image here).

I have tried several iterations within CP to apply a threshold that produces a masked image, but it also tends to remove the cell nuclei signals from the image since they have similar intensity to the exterior of the well. I cannot use a predetermined mask as the well locations are variable, and we lose a signifiant portion of each well if we use a single masking template. Here is the pipeline I have been trying out, based on the results from this thread.

Any help or guidance would be very welcome! Thank you so much in advance!

Best,

Stefan

Hi Stefan,

I had better luck identifying the well as one big object with IdentifyPrimaryObjects.

Pipeline is attached so you can see if it works for a range of your images.
Crop_Test_I2.cppipe (12.7 KB)

That’s a fascinating approach! Thank you so much for recommending it! I think with some refinement I might be able to get it to work. I really appreciate the feedback!

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