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.

Mody, T. A., Rolle, A., Stucki, N., Roll, F., Bauer, U. and Schneitz, K. (2023). Diverse 3D cellular patterns underlie the development of Cardamine hirsuta and Arabidopsis thaliana ovules. bioRxiv doi: 10.1101/2023.12.06.570408.

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 (currently not public)
     • 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 . .