I’ve been working on a pipeline for a while now and I’ve been using this forum to answer a lot of my questions, but I still have a couple of unresolved issues that I was hoping someone would be able to help me with. The purpose of the pipeline is to detect the nuclei, vimentin staining, and e-cadherin staining, and run some measurements on those detected objects. I attached a couple different sets of images that I would be analyzing (c1- vimentin, c3-nuclei, c4-ecadherin).
- First, one of the issues I’ve really been struggling with is I have a lot of image to image variation. So for example, in one image set the e-cadherin staining may be more junctional and there may be more tight junctions present than in another image set. So far, I have been only analyzing images that are visually similar to each other at the same time, and have also incorporated the editobjectsmanually module at each step into my pipeline. This takes a lot of time and I can really only run a couple of image sets together. I was wondering if there were any ideas on how to improve this method or to be able to analyze all my images at one time?
- Additionally, I would ideally like to be able to detect the number of cells that are expressing junctional e-cadherin. In some image sets all of the cells have junctional ecadherin, but in other image sets, only a couple of the cells have junctions. I was wondering if there was a way to quantify the number of cells that are expressing highly fluorescent borders (junctions)?
Here is a dropbox folder with the pipeline I’ve been working with and two sets of images (C1- less ecad junctions, and D1- more ecad junctions):
dropbox.com/sh/z5mcsnf6imbk … PiFMa?dl=0