Dissecting glial scar formation by spatial point pattern and topological data analysis - Github Repository

This repository is linked to the article "Dissecting glial scar formation by spatial point pattern and topological data analysis" published in XXX (DOI: LINK). If our approximation and code is valuable for you, we kindly ask you to cite the article mentioned above.

Description

We conducted Point Pattern Analysis (PPA) and Topological Data Analysis (TDA) in microscopy brain images derived from ischemic animals (MCAO model) at different time points. We analyzed the spatial arrangement of GFAP and IBA1-expressing cells forming the glial scar. This repository aims to make our approach fully reproducible. Find the whole project repository in https://osf.io/3vg8j/

Prerequisites

Install R (https://www.r-project.org/) and RStudio (https://posit.co/). The "2022_GlialTopology_Notebook.qmd" file contains a chunck for the installation of all the required R-packages.

How to use it

1. Download the repository. Empty folders are paths to store new generated tables and data.

2. This repository uses research data available in https://doi.org/10.5281/zenodo.7876620. For a full execution download the Zenodo repository and paste the unzipped "QupathProjects_5x" and "QupathProjects_10x" in the working directory.

3. Execute the "2022_GlialTopology_Notebook.qmd". We recommend doing so (initially) chunck by chunk as we expect errors arising from missing paths to the working directory. Please create folders or change paths at your convenience.

4. If errors occur, please do not hesitate to report them or contact us.

Files and folders

1. BayesianModels: Empty folder used to store Bayesian models generated by brms
2. Hyperframes: Empty folder used to store point patterns
3. R_Functions: Folder containing plotting functions
4. ResultsTables: Empty folder used to store generated data
5. SummaryTables: Empty folder used to store generated data
6. TDA: Folder containing .py (Python) scripts for TDA
7. 2022_GliglTopology_Notebook.qmd: Quarto notebook emplayed for data handling and analysisEmpty folder used to store Bayesian models generated by brms
8. references.bib and nature-communication.csi are files generated by the notebook to generate bibliographic references using the Nature Communications style.