First message in the forum, I am a bit stuck trying to automatize a relatively simple calculation in my images and wonder if you could help with it.
So, here is my problem: Dataset with some hundreds of images with single cells, they have a spherical body and most of them have a protuberance. Target is to measure the radius of the main body, plus the length and diameter of the protuberance. I can do this one by one and not very accurately y hand, but I would like to ask if there is some script/plugin out there that can do this automatically, so I can run a macro on my dataset later.
My scripting skill is very limited, but I could manage to put pieces together if you know something that should work with the problem.
Goals: automated selection of body and protuberance, automated measurement of body diameter, protuberance length and protuberance diameter (perhaps measurement of diameter at several parts of protuberance, to better calculate area later)
I can put all my files in a single stack, and segment them so there is a single object in each image (see example). But I do not know how to automate identification of body and protuberance, and then automate the measurements. I am initially exploring fiji, but other open source softwares are welcome if you know adequate scripts in them.
Thank you very much in advance!