I am staining Mouse Cardiac endothelial cells with Fluorescein Diacetate and Propidium Iodide (FITC for live cells) (propidium iodide is a nuclear dye for dead cells). How do I create a pipeline for these cells so I can analyze number of stained cells and morphology.
Welcome! Please have a look at this post first: Before Posting… .
(1) Have a look at example pipelines: cellprofiler.org/examples.shtml . Do any come close to what you want to analyze?
(2) Post your pipeline attempt (it makes it easier for us to help you, and also lets us understand where users might go be guided more judiciously)
(3) Describe what you mean by “morphology” – area, skinny vs. round, textured, etc?
(4) Post some example images! They should show the range of features you want to quantify.
Here are some pipelines, one of them I made watching the introduction and another is an FDA PI from a forum post I found. I have attached a file containing the FDA-PI stain. I can add more if that would help. I’m not looking at morphology specifically in this experiment, but will further down the line (in the next few weeks).
You attached the output files, but not the pipeline(s) themselves. The pipeline should have an extension like .cppipe or project files are fine too (.cpproj) as long as we have an image, which you did post. Can you post your pipeline? Thanks!
For some reason they won’t upload on the forum. I get this popup: “Sorry, the file you are trying to upload is not authorized (authorized extension: .bmp, .gif, .jpeg, .png, .tiff, .webp).”
I just added .cppipe, .cpproj, and .zip. Sorry about that, we’re just getting this new forum tuned up!
No problem, thank you for adding it. Here are my attempted pipelines:
pipeline_FDA_A 14-1.cp (10.0 KB)
I can’t download the pipeline rfinnegan2 posted. Can .cp be added as an authorized extension?
Afaik, authorized extensions are only for uploading. I added ‘.cp’ awhile ago as an authorized extension which that let the user upload. But I’m stymied as to why it is not letting us download them (I cannot either). Looking into it…
Any advice on settings to use for this?