Spatial and density calibration from TIFF files to ImageJ

Posted by Davide Guarisco on Oct 19, 2015; 4:02am
URL: http://imagej.273.s1.nabble.com/Spatial-and-density-calibration-from-TIFF-files-to-ImageJ-tp5014677.html

Hello,
        I have tried to find this information elsewhere but was not successful, so I am posting here.

I am writing a Python script that converts a proprietary image format into a TIFF file, which I subsequently intend to open in ImageJ. I want to transfer the information regarding both the scaling (spatial calibration) and density (Z-values) via the TIFF file.

I tried to determine how ImageJ saves this information by looking at the files generated before and after setting a scale and adding a calibration. For the Z scale, it seems that ImageJ just adds the following to the Image Description (e.g., in the case of a linear calibration):

cf=0 c0=0.0 c1=0.3326 vunit=nm

For the spatial calibration, via searching this list, I was able to find that ImageJ uses the x_resolution, y_resolution TIFF tags. This works, except that the unit is not set. How can I communicate the unit of the spatial resolution? Notice that a standard TIFF tag is unit_resolution. However, this only supports three values (1=none, 2=inch, 3=cm).

To save the TIFF files from Python there are many possibilities. I am leaning towards tifffile.py for now. If anybody has an opinion on this, please let me know as well.

Thank you in advance.

Davide

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