FilterObjects: Is there a way to filter mean intensities by percentage of the maximum intensity?



My experiments are never exactly the same so keeping the intensity threshold the same absolute value across all sets of images is not possible. Therefore, I want to keep the percentage of the maximum intensity the same throughout all my experiments as a control instead.

Any help would be greatly appreciated :slight_smile:


The maximum intensity… of that image? Of the whole batch? Something else?

The first is easy (just use RescaleIntensity), the latter is not difficult but is more steps- you’ll have to run a pipeline on each batch with MeasureImageIntensity and an Export module to figure out what the maximum for that batch is, then either tweak your pipeline for each batch or pass that maximum value in as a piece of metadata (again, using RescaleIntensity) .