I have carried out a cell painting assay (staining the nucleus, ER, mitochondria, golgi, F-actin and nucleoli using six dyes) and used the example features pipeline from the Carpenter lab, which gives a great starting point for data extraction.
So far I can identify nuclei, cells and cytoplasm and extract data on object intensity, distribution and texture etc. However, I also need to identify the ER, golgi, mitochondria and actin! I have tried using the speckles module but cannot seem to do this for golgi and mitochondria.
Has anyone had experience of defining these organelles as objects and extracting data from images of these organelles? I have attached the pipeline I have so far, any help would be really appreciated!