I was impressed by the CellProfiler approach and i would like to implement it in the analysis of mammary whole mount. From my reading through the manuals I know that there should be a way to create a pipeline that work but I spent much time with no perfect success that suits my needs. Basically, mammary gland consists of ducts, branches and terminal buds which are located at the end of the side branches. In the whole mount, the mammary gland is stained so we can see these different structures. The ducts are lightly stained while the terminal end buds are darkly stained. Moreover, there will be a centrally located darkly stained big structure which refers to the mammary lymph node. The idea behind whole mount analysis is: 1- Get and estimate of the number and size of the terminal end buds. 2- get and estimate of the area occupied by the mammary ductal system. 3-Excluding the mammary lymph node from all these calculations.
I will really be so grateful for any kind input.
Please have a wonderful day
Did any body have suggestions regarding this topic.
Any starting help will be really appreciated.
I’ve put together a pipeline which should get you started. Look at the module notes at the top of the module settings to get a sense of my thought process in putting it together if you need to make tweaks.
It does the best it can with feature detection on the basis of a single stain. Ideally, things would work better if you have access to a counter-stain for the features of interest (knowing full well that that is not always possible )
2012_08_10.cp (15.8 KB)
Thanks so much for your reply. The pipeline makes a very good sense with the image attached. It is very helpful starting point. I will go through it with more images and see how it goes from in there.
Thanks so much again. I really appreciate it