Converting between ImageJ ROI and GeoJSON format

[oeway (Wei Ouyang)]

Wondering if anyone have a ImageJ plugin, macro, or Python script which allows converting between ImageJ ROI file and GeoJSON format (which is used by, for example, QuPath, and we use it in Kaibu).

I would like to use it in ImageJ.JS so we can import GeoJSON annotation files.

[petebankhead (Pete)]

I’m not aware of anything – QuPath should contain the necessary logic, but it moves through its own intermediate representation so I suspect you’d want to skip that for something more direct.

I expect conversion to an ImageJ ROI should be relatively ok, since the GeoJSON specification is nicely-written.

The relevant bits in the QuPath code:

• Geometry to QuPath ROI (mostly similar to ImageJ)
• QuPath ROI to ImageJ

Note that, at the end, for complicated stuff it creates a java.awt.Shape and generates a ShapeRoi from this… leaving a lot of the most difficult logic up to Java AWT. To help, I used the ShapeWriter from JTS: (source here).

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Conversion from ImageJ to GeoJSON is likely much more awkward.

The relevant bits of the QuPath code:

• Convert from ImageJ ROI to QuPath ROI
• Convert from QuPath ROI to JTS Geometry
• Create the GeoJSON

By far the most awkward / error-prone part is handling multipolygons – particularly as they can contain holes, and (most evil of all) positive regions nested within holes. Earlier QuPath pre-release versions continually failed with some obscure shapes, but I think the logic is pretty robust now.

The most general way I can think of achieving a conversion is:

• Handle the ‘easy’ cases (lines, points, rectangles… ellipses aren’t really supported)
• Convert any complicated areas (including ImageJ polygons, since they may have self-intersections – forbidden in geojson) into a ShapeRoi and then:
  • Get a java.awt.Shape from the ShapeRoi
  • Generate an java.awt.geom.Area object (since this has some guarantees)
  • Use the PathIterator from the Area to generate polygons… see here for info on how I did it in the end

I fould JTS useful/indispensable in this, but you should avoid its unreliable ShapeReader – which only works in the easy cases.

[oeway (Wei Ouyang)]

Hi @petebankhead Thanks a lot for these pointers! this is super useful, I will try to see if we can make a ImageJ plugin for importing and exporting GeoJSON files.