i want to align 2D slice image to the MRI space and having difficulty getting information about Z axis (and also some dangling parameters in X and Y):
Given the slide image 102058920, which belongs to the root specimen H0351.1009, i take two points at the image’s extremes:
[30287, 41968,0] (width and height at the original scale) and apply the
tvr part of the specimen’s 710418 (the direct parent of this section image)
alignment3d transformation to them (and divide by 1000, as those are micrometers and the MRI is in millimeters).
The resulting coordinates give me a kinda plausible positions within the specimen’s MRI volume, but the two problems remain:
- Z coordinate is not affecte by this transformation (it’s still 0)
- there are non-zero attributes
parent_z_coordfor each specimen from the one specified in the slice image - 710418 - all the way up to the root one - 708900. An i’ve also encountered slice images linked to the specimens without
alignment3dattribute at all, so the should presumably be aligned via this coorinates only
Is there some kind of a documentation of how these alignment are properly calculated?
Or is there a source code for the API (not the SDK) which i can look into and find it myself?