Tissue Image ToolKit

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Tissue Image Toolkit (TimageTK) is a Python package dedicated to image processing of multicellular architectures such as plants or animals, and is intended for biologists, modelers and computer scientists.


The package provides the following main functionalities:

Image filtering

Linear filter operators such as: Gaussian, gradient, hessian, laplacian, …

Mathematical morphology

Morphology operator such as: erosion, dilation, opening, closing, hat transform, sequential filters, …

Image registration

Linear and non-linear block-matching registration, transformation operators, sequence registration, multi-angle fusion, …

Image segmentation

h-transform, connected component labeling, watershed, …


Stack browser, orthogonal views, projection maps and other GUI.

Batch processing

A simple data model allowing to perform batch processing of large of dataset.

Images and other data structures can be rendered using the visualization functions we provide. However, if you are less experienced with code, using a dedicated interactive image visualization software such as Gnomon or Fiji is recommended.

Written in Python, TimageTK leverage the work of some of the most standard Python libraries such as:


Jonathan Legrand
Lead developer A B CNRS

Christophe Godin
Coordinator A Inria

Grégoire Malandain
Coordinator C Inria

Teva Vernoux
Coordinator B CNRS

Guillaume Baty

Guillaume Cerutti
Contributor A INRAe

Sophie Ribes

Active research teams

A Inria team Mosaic, RDP-ENS Lyon, UMR5667.

B Hormonal Signalling and Development team, RDP-ENS Lyon, UMR5667.

C Inria team Morpheme, Sophia Antipolis.

Source code

Inria GitLab repository

The Inria GitLab repository of TimageTK is maintained by members of the Mosaic team. Use the Issues section to contact us if you have difficulties or issues.

GitHub repository

The GitHub repository of TimageTK is not maintained anymore, but is kept for historic reasons.


Some non-standard libraries, developed by other research teams, are used in this project, such as:


Follow these contribution guidelines if you want to participate to TimageTK development.