First, let me thank for all the great work that you guys are doing on CP. I absolutely love it and I became a self-appointed CP evangelist in my group
Here’s my question. I’ve got two masks from MetaMorph (I use it to identify neurite outgrowth per cell, a functionality that CP lacks at the moment, I believe):
- neurite mask with shades of gray that correspond to object numbers in MetaMorph xls file,
- nuclear mask, which is just binary.
In CP, I measure fluorescence intensity in nuclei from other tifs with appropriate staining. In order to measure nuclear fluorescence, I need the nuclear mask with annotated objects. Needless to say, I need to keep the same object annotations. I simply multiply the neurite mask (which already contains object numbering) with the binary nuclear mask. The problem is, that when I do it in CP, I obtain a new image. How can I extract object information within the pipeline from that image? It’s possible to do that at the beginning in NamesAndTypes when I load an already saved image and load it as Objects. But I couldn’t achieve that without saving the multiplied image and re-loading it.
Another similar issue concerns retaining image annotations after applying a filter. In CP, I use the annotated neurite mask, apply a median filter to get rid of neurites and just have an annotated mask with cell bodies. Now I’d like to run shape&size module on that new mask. But again, since the result of filtering is a new image, how can I extract image numbers from there, within the pipeline?