CellPose Napari plugin does not consider scale of original layer

[sebi06]

Hi all,

I just tested the CellPose plugin in Napari and it seems the its output does not have the same scale a the original layer (to be segmented): For a detailed description check:

https://forum.image.sc/t/cellpose-napatri-plugin-does-not-consider-scale-of-original-layer/70919?u=sebi06

[aeisenbarth]

Similar issue, our segmentation results are not properly overlaid with the input, but offset to the origin. In our case, input images are registered to a global coordinate system, making use of affine transforms, which can include an offset and a rotation.

The scale property is just a shortcut to one aspect of the affine transform. The whole affine transform needs to be considered. Since the output is in the same coordinate system as the input, it should be the same transform matrix (possibly one has to adjust for different number of dimensions in case singleton dimensions get dropped).