I am trying to construct a pipeline to compare staining of yeast cells.
This is the experiment as I understand it.
I have yeast cells grown under 2 stress conditions (salt/no salt).
I have been given 4 images all in color that I convert to grayscale:
a white field image
a blue DAPI stained image as a control for nuclear staining.
a red image which is a transcription factor tagged with mCherry
a green image with a transcription factor tagged with GFP
I need to figure out:
- What fraction of cells have a nuclear signal?
- What are the distribution of nuclear fluorescence values for stained nuclei?
- When either of the transcription factors are in the nucleus, what fraction
of the time are both transcription factors in the nucleus?
I have attached the images and my pipeline.
I see on the forum that one is supposed to ID the nuclei first,
I have managed to do that, but I am having issues with getting
good cell identification, there are more cells divisions than expected.
How can I go from identifying nuclei to getting good cell id?
I switched to manual for the the first nuclei because I was unable
to get the auto methods to work.
I have looked at and tried several of the pipelines listed on the
forum and tried some of the tutorials. I find them confusing,
is seems there are so many options and everyone does something
a bit differently. I have attached my latest pipeline
the images are available via box at:
MyTest-Pipeline.cppipe (60.7 KB)