What is the best method to correct for loss of signal intensity in the Z-axis? I am having trouble with image segmentation/ pixel classification (using ilastik or with thresholds) due to intensity decay through the Z-stack. While I do not need to quantify intensity itself in the images, I do need to quantify the number, area and shape of classified puncta and Z-scatter/aberration is interfering with classification due to varying intensity. I came across this publication and I was wondering if anyone has tried or would recommend the Intensify3D program: https://www.nature.com/articles/s41598-018-22489-1
This post seems relevant: Compensating brightness attenuation in a confocal stack?
Is there any consensus/optimal method for this sort of correction (in any program, doesn’t need to be program-specific)?