OrganAxis is a computational approach for the construction of a Common Coordinate Framework (CCF) from a set of spatial landmarks.
Key features:
- Derived purely from the reference image. This makes it universally applicable across any spatial platform and at any resolution.
- Straightforward approach that significantly reduces the risk of double-dipping (e.g. it is not derived from high-dimensional gene space).
- Allows multisample “diagonal” integration while preserving continuous spatial information.
- Allows modelling of linear and non-linear spatial associations to account for local and global tissue environments, e.g. cellular neighbourhoods and anatomical structures.
- Hypothesis-driven: Prior knowledge about the tissue in question is needed to derive a biologically robust and meaningful axis.
OrganAxis is implemented to derive the human thymus Cortico-Medullary Axis (CMA) here - https://github.com/Teichlab/thymus_spatial_atlas/tree/main
Note
This project is under active development.
.. toctree:: introduction annotation_and_sampling Model formulation Model application
image credit: DALL-E
| Authors: | Nadav Yayon, PhD |
|---|---|
| Version: | 1.1 of 12/04/2024 |
| In memory of: | Daniele Muraro |