I only began using cell profiler a few weeks ago and it has been great. I have problems using the classify module. For a start, I loaded five different color images(later on I will increase the number of images to about 300) and I have exported the .hd5 file from ilastik (I had use ilastik to train and classify them). When in the classify pixel module, I import it the .h5 file. But it keeps giving me some funny error message I don’t understand whenever I run the pipe line. Please I need a step by step guide on how to analyize lots of images using the classify pixels module. I know I’m doing something wrong but can’t figure out what.
Another question, in the identify object module, is it the probability output map of the classify pixel module or the input image of the classify pixel module I’m to use as input to the identify object module? How can I identify objects in say 300 images using this method?
Kindly find attached the errors and my pipeline.
Thank you as I look forward to hearing from you guys…
pipeline.cppipe (5.93 KB)