Development of this tool has now been moved to BrainGlobe/slicereg
Registration of 2D sections to a 3D volume
The aim of slicereg is to be the 2D companion of
amap to provide
registration of 2D brain tissue sections (of any kind) to a 3D brain atlas
such as the Allen Reference Atlas.
Features (e.g. labelled cells) in these sections can then be transformed into a common coordinate space of the brain atlas, and features from multiple samples can be visualised together (e.g. in brainrender).
All results will be compatible and interoperable with cellfinder, amap, neuro, brainrender, and ideally any other similar tools.
Contributors are more than welcome, please see the contribution guide and the roadmap.