I have scanned the forum but could not find any relevant question. Has anyone successfully converted the coordinates from elements file which is exported via from PALM Zeiss system into ImageJ coordinates?
I am working on a project in which a user obtains two samples, one stained and one unstained using the Zeiss Laser Microdissection. We then draw a ROI on the stained sample (using Zeiss software) and export the coordinates in the form of an elements file. This is a text file containing all the coordinates of the ROI outline and some metadata. Externally in FIJI, we try to align the stained and unstained samples via registration. Using the obtained transformation, we transform the coordinates in the elements file from the stained sample. We write this to a new elements file and import it into the Zeiss system. This transformed ROI is then placed on the unstained sample. In the ideal case, it should be at the same location as in the stained sample.
After a lot of experiments and tests, I have managed to normalize the coordinates in the elements file to the stage coordinate system after following https://github.com/fabricecordelieres/IJ-Plugin_PALM_Zeiss_workflow/blob/master/Docs/Poster_Szeged-Hungary_NEUBIAS_2018.pdf but after that its still a mess. The ROI is clearly offset which could be corrected by hardcoding some value. But what I am struggling with is the scaling. Some images below illustrate the problem.
How the ROI looks like in Zeiss (Rectangular ROI on left):
How the same ROI shows up in FIJI after normalizing wrt stage coordinate system:
Any help is appreciated! Thank you!