Code used within the Arkell lab that warps a provided single organ mask/label to orientated uCT scans of 12.5 dpc embryos and performs basic volume calculations I am hoping to use the Pydpiper environment to create a pipeline for organ analysis within 12.5 dpc stage embryos. Current analysis within Pydpiper requires the generation of average models. This pipeline, however, will calculate absolute organ volumes within each scan and then normalise to the total whole embryo volume. Direct statistical analysis of embryo volumes between groups should be able to be performed after whole embryo normalisation (i.e. dividing the organ volume by the whole embryo volumes and regressing by whole embryo volumes.
Dependencies: AntsRegistration Package (https://github.com/ANTsX/ANTs)