I am trying to count the number of DAPI stained nuclei on polymer spots. Some of these spots autofluoresce, creating an irregular background and false positive objects in IndentifyPrimaryObjects.
I am using OTSU>Three Classes for my thresholding and have played around with the threshold correction factor but I lose some nuclei which have a dimmer fluorescence when I increase this.
FilterObjects based on Eccentricity has removed many artifacts but I am still getting some.
I have attached a selection of images which mostly contains ones for which I get background errors but also few images that don’t have any background issues.
Currently using CellProfiler 2.2.0 on Win10