Dear CellProfiler development team,
this is a feature request.
I recently successfully integrated the “CLAHE” contrast adjustment macro using RunImageJ under CP 2.1.
With this, the CP module “UnmixColors” provides better results. I still have some issues when separating Masson’s Trichrome histology images resulting “magenta/red” and “blue” sometimes the same gray values.
ImageJ’s/Fiji’s color deconvolution module (plugin for ImageJ, integrated in Fiji) provides better results in separating true “red” from true “blues” (or other combinations of colors, deconvolving into 2 fully separated channels, leaving one as “leftover”).
The plugin module fails to work with the RunImageJ module, but would be anyways better if natively integrated.
Is this possible and supported for version 2.1?