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OME model (specification, code generator, implementation)
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Unknown units: 1/nm #186

Open alexandrebastien opened 6 months ago

alexandrebastien commented 6 months ago

Transmission electron microscope can produce diffraction image often called SAED. These would be in “1/nm” units since they are from the conjugated plane. When we open such a file (*.dm4) in Fiji with Bio-Format, the following warning is displayed: [WARN] Not adjusting for unknown units: 1/nm If we go in “scale bar”, the unit was simply replaced with microns, which is misleading and should not be used. I suggest that the 1/nm unit could simply be included as a valid unit in Bio-Format. It's often presented with parenthesis to avoid confusion "(1/nm)".

Here's an exemple of how an analysis of these images could be done. Briefly, length are kept in reciprocal (1/nm) units, then the user would invert them to obtain the d-spacing which is the wanted value is those analysis.

In my case, the camera used to produce the images is a Gatan OneView, filetype is dm4, Fiji/ImageJ 2.14.0/1.54f; Java 1.8.0_322 [64-bit]; Windows 10

imagesc-bot commented 6 months ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/wrong-units-from-tem-diffraction-image-of-gatan-camera-dm4/92349/7

melissalinkert commented 6 months ago

Thanks, @alexandrebastien. Transferred to the https://github.com/ome/ome-model repo, as this is something that would need to be updated in the OME schema (specifically, the UnitsLength enum). Once the schema is updated, Bio-Formats would be able to make use of the new units more or less automatically.