Invert grayscale in cellprofiler


I am trying to use probability maps generated by Ilastik in Cellprofiler. Unfortunately, the colors are the other way around. My cells are black as opposed to white. Are there options available to change these colors?



Hi Janne,

In the module ImageMath one of the operation options is “Invert”. This should work for you.

Just to let you know you will actually be changing the values of the image not just the colours as it sounds like your Ilastik output has the cells marked as background and the non-cell area marked as foreground and that’s what you need to change.