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labsyspharm / minerva-author

Tool to create images and configuration files for Minerva-Story
MIT License
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Allow pixel size to be set, manually or automatically #55

Closed jmuhlich closed 1 year ago

jmuhlich commented 1 year ago

We should read the pixel size (OME Pixels.PhysicalSizeX and ...Y) from the input ome-tiff and place it in an editable field on the Sample Info tab. This should be presented as pixel size in microns in the UI -- microns is a reasonable scale for our target audience. This value should be written (inverted of course) into the published exhibit.json under the PixelsPerMicron key to configure the scale bar. Well-written ome-tiffs will then automatically get a scale bar in their stories, and users can manually edit or override that value if it's incorrect or missing entirely.

jmuhlich commented 1 year ago

Let's bump this to high priority! We apparently have a lot of stories going out without a scale bar.

jmuhlich commented 1 year ago

How to extract the pixel size in microns:


ome.images[0].pixels.physical_size_x_quantity.to('um').m```
thejohnhoffer commented 1 year ago

Resolved in Minerva Author v1.14.0