I’m trying to do an automatic stomata phenotyping based on this paper :
I don’t have much knowledge in programming and I don’t really know where to begin.
I’m pre-processing images following instructions in the paper :
- Setting image 8-bit grey scale
- Applying a gaussian blur
- Substracting the resulting image to the original one
- Making it binary
And I end up with this :
Result of 04032019_KO5_RC_2-1.tif (1.3 MB)
Here is the original one :
I can create a macro to easily automate this part and run it in batch using the macro recording tool.
After that step, I’m launching the Template matching pluging from Fiji (https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin
Using templates of Stomata like this one :
Template_KO_test.tif (3.1 KB)
It works just fine but it only counts stomata in the exact same positions. The reference paper advices to multiply templates and make them rotate to have better results. They also implements functions to avoid false positive. But here is the problem, the pluging can only run with one template and once you want to run it again with an another template, it reinitialize all the data. So the solution could be asking Fiji to keep data and overlay until you process all the desired templates with different angle. This is the part that goes beyond my habilities in programmation.
Here is what I manage to understand for the next part, once the pluging recognize stomata they use Plot Profile (Analyze > Plot Profile) within ROIs to obtain certain values like stomata apertures, stomata widths and stomata lenghts. I know how to do it using Fiji but I don’t know how to do it within a macro with Fiji language.
I know that there is a lot of programmation work here but if you have at least intels to help me in this work that could be really great.
Thanks a lot,