Dear All,
Currently I am playing around with ImageJ in order to help me with a fluorescence image analysis.
So I have cells under two conditions, condition one of which there is a Collagen1A1 staining purely intracellular/ cytoplasmic. Condition two there are strands coming off cells, making networks etc.
Total fluorescence doesn't distinguish anything as condition one has a higher threshold of intracellular pixels than condition two. Further total fluorescence per cell isn't indicative of what I want to show.
Seen as I have 400plus images and would like a fair automated analysis, I've been playing with using 3D-surface plots, but not sure how to quantify "connections' between peaks..
Then on further suggestion, a friend suggested using SurfCut but I get an error with the plug-in (pic included)..
Any ideas? Suggestions? Recommendations would be really appreciated :)
I think if I can't do something, I will just take (pseudo)random sections of the images and manually count the number of bundles leaving each cell.. something like that.
Many thanks in advance for your replies,
Cengiz
I appreciate your works very much. I think you can get your solution easily if you join ImageJ mailing list. Because, the ImageJ mailing list is a discussion group for ImageJ users and developers.
You will get access form here, https://imagej.nih.gov/ij/list.html and their email address is "[email protected]".
I am pretty much sure the discussion group will give you better solution.
Thank you. Stay safe and warm.
Many thanks for the reply.
I have figured something out using standardised ImageJ analysis normalising intensity, removing background and counting the number of and size of fluorescent particles!
Having a look through the ImageJ forums, I think there could have been a more elegant/ robust method for analysis. But I am not familiar with MatLab (or any programming language!! ) .
Exciting data as well, hope my supervisor and the reviewers agree!!
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