Error in MaskImage module when trying to count colonies based on yeast colony tutorial




I am performing an assay that requires counting of fixed, crystal violet stained colonies in a 10cm plate format (see example picture of plate and plate template below, with original picture converted to grayscale to reduce processing time), ideally in an automated, non-biased way. Because the colonies are similar to those described in the yeast colony counting tutorial, I have attempted to adapt that pipeline for my purposes, with some simplifications since I do not particularly care about distinguishing color. I have attached the .cpproject file as well. The first few steps seem to work well (CorrectIlluminationCalculate, CorrectIllumination Apply, and Align [though this step is quite slow]) but when it gets to the MaskImage step I get the following error:

“Error while processing MaskImage: boolean index did not match indexed array along dimension 0; dimension is 2722 but corresponding boolean dimension is 2681.”

I am not sure why this is, as the plate template was derived from this particular image, and the alignment step should fix this, I thought? Any tips or suggestions would be appreciated, as I would like to get the pipeline working so I can launch it on all my images.


transposase_assay_test_v1.cpproj (981.4 KB)


Hi Rachel,
You’re aligning the picture to the template- try swapping the order and aligning the template to the plate and see if that helps. Good luck!