How to open an overlay from ImageJ in Matlab
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Hi everyone. I have traced a cell in ImageJ and saved the tiff file with the overlay. I'm wondering how I can open this tiff file in MATLAB and use the outline to measure values from. Essentially, I have saved the tiff file with the overlay and when I open it in MATLAB the overlay is not present/visible. Thanks so much for your help!
2 Comments
taylor hietpas
on 29 Jun 2018
I have precisely the same question. Any luck?
Matthew Isaacson
on 10 May 2020
Years late, but here's what I found. The problem is that reading overlay data is not supported by the "libtiff" library that Matlab uses to read tiff files. If you absolutely needed to solve this problem solely in matlab, I think you'd have to find a way to modify the library (see here: http://www.libtiff.org/internals.html) and add a few new lines into the matlab "tiff" function to support the overlay tagIDs (50838 and 50839). Though an easier workaround is just to open the tiff in imagej and save the overlay data in an xls file (Image>Overlay>List Elements) and open that up in matlab.
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