Welcome to OrganAxis documentation!

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.

Contents

• Introduction
  • Common Coordinate Framework
• Prerequisites for the establishment of a CFF
  • Consistent tissue annotations
  • Spatial sampling resolution
• Organ Axis model
  • 1. Definition of distance function (D), spatial location (P), and structure (S)
  • 2. Mean distance of KNN points to P
  • 3. Inferring the normalised relative distance to a boundary
  • Exploration and intuition from simulations of K and grid resolution on axis function
• Thymus morphology and T cell maturation
• Motivation to construct the Cortico-Medullary axis
  • Full model assembly and binning

image credit: DALL-E

Authors:

Nadav Yayon, PhD

Version:

1.1 of 12/04/2024

In memory of:

Daniele Muraro