BodenmillerGroup / immucan-roi

IMMUcan ROI selection using napping and napari-roi
MIT License
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mirrored czi and panorama #12

Open SchulzDan opened 2 years ago

SchulzDan commented 2 years ago

currently the czi and panorama are not oriented in the same way - basically mirrored. Would be nice to have this fixed at some point.

jwindhager commented 2 years ago

mirrored in y-direction I assume?

SchulzDan commented 2 years ago

yes, y direction

jwindhager commented 2 years ago

That's because the MCD coordinate system is in fact inverted (non-standard). Little to be done about that in principle, but I can calculate the coordinate systems back & forth in the MCD (however, the coordinates displayed in napari will be wrong then, just FYI).

SchulzDan commented 2 years ago

What if we flip the czi coordinates for visualization since it is more unlikely that someone will use those actively?

jwindhager commented 2 years ago

Currently not possible in a clean way (i.e., without changing data coordinates), see https://napari.zulipchat.com/#narrow/stream/212875-general/topic/coordinate.20system