TimageTK - Geometry

TimageTK - Geometry (Tissue Image ToolKit) is a Python package injecting tools from the computational geometry field into the analysis of images of multicellular tissues, both in 3D and 2D.

Overview

The package provides tools structured around 4 main functionalities

Image Surface

Create triangular meshes representing the surface of tissues (from raw or segmented images) or the interfaces between adjacent cells (walls)

packages/image_surface.html

Tissue Complex

Topological representations of tissues as cellular complexes: simplicial complexes of cell adjacency and (triangulated) polyhedral complexes of cell geometry

packages/tissue_complex.html

Features

Compute geometrical features on cells and walls using mesh representations (normals, curvatures) and process features using advanced operators

Signal Quantification

Combine intensity images and mesh representations of the tissue to quantify signals in elaborate ways (normal sampling, wall signal polarities)

Getting started

Installation

TimageTK - Geometry is made available as a Conda package, and can be easily installed using the following commands:

conda config --add channels conda-forge
conda config --add channels mosaic
conda config --add channels morpheme
conda install timagetk_geometry

For a more advanced usage, have a look at the Installation Guidelines

Examples

In the Examples section, you will find various working examples detailing the basic usage of the library.

Related libraries

TimageTK - Geometry constitutes an extension to the TimageTK Python library and mostly provides functions that operate on its major data structures (SpatialImage/MultiChannelImage, TissueImage2D/TissueImage3D), either to extract topological objects (meshes and complexes) or to compute geometry-dependent features.

For the computational geometry part, the library essentially relies on the CellComplex Python package as well as on some algorithms from the VTK library through the PyVista Python API.

API

Documentation