I’m trying to classify cells and nuclei to count nuclei per cell. The nuclei are unlabeled and dark. I ran pixel and object classifications separately. My pixel is pretty good and I can export those prediction maps. I could just threshold in imageJ to count but I want to try to classify objects in Ilastik.
I have 3 labels in pixel: background, cells, nuclei.
Then I thresholded in objects Label 1 and cells and label 2 as nuclei.
How can I export this as a 2 channel tif for processing in imageJ?
I can export an 8 bit tif of just nuclei (or the last think I thresholded). PS my raw data is a single image, no time series.
So how to do get a binary image with two channels, representing thresholded objects for the cells and nuclei (blue and the pink)?