I am analyzing organoid sections and am using a mask to map out the area of the organoid and then identify nuclei and astrocyte staining within. While my mask blocks out noise (dots outside of the main clusters), there are some sections in which the actual organoid area is masked out. Any suggestions to improve this?
My approach is IdentifyPrimaryObjects (to get the organoid object) → ConvertObjectsToImage and MaskImage → then I use IdentifyPrimaryObjects with the MaskImage output to identify the nuclei and astrocytes in the masked out organoid area.
I’ve attached my pipeline and a photo of two different organoid images (left: unsuccessful mask, right: more or less successful mask, there is a missed section near the top of the organoid section).
Thank you, your help would be much appreciated!