fabian-roll/NADO

NADO: Nerve-based topological analysis of 3D digital ovules

NADO: Nerve-based topological analysis of 3D digital ovules

The code in this repository accompanies the following joint work.

Tejasvinee Atul Mody, Alexander Rolle, Nico Stucki, Fabian Roll, Ulrich Bauer, Kay Schneitz; Topological analysis of 3D digital ovules identifies cellular patterns associated with ovule shape diversity. Development 15 October 2024; 151 (20): dev202590. doi: https://doi.org/10.1242/dev.202590

Usage

The topological analysis can be reproduced as follows.

1. Download the git repository and place the ovule source data in the data/ folder as described in data/folder_structure.txt.

   • Arabidopsis
     • https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST475
     • https://www.ebi.ac.uk/biostudies/studies/S-BSST513
   • Cardamine
     • https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD957

2. Install Docker and execute the following command inside the repository to compute the nerves associated to the TIFF files.

   $ docker build -f compute_nerves.Dockerfile -o . .

3. Execute the following command inside the repository to reproduce the topological analysis and save the output to the output/ folder.

   $ docker build -f analysis.Dockerfile -o . .