This repository contains the material associated with the StarProtocol for Point pattern analysis (PPA).

Atlas_Regions.csv is a dictionary containing brain area names and acronyms. It is useful to set up an automatic pipeline for cell counting in specific regions using QuPath. SingleImage_Processing.qmd Annotated Quarto notebook (https://quarto.org/) for single image processing. This notebook was created using R. BatchImage_Processing.qmd Annotated Quarto notebook (https://quarto.org/) for batch image processing. Please note that this notebook is associated with a recent publication by our research group (https://www.biorxiv.org/content/10.1101/2023.10.04.560910v1).

To run the complete protocol as stated in the article, the user may need to install:

Quarto: https://quarto.org/ QuPath: https://qupath.github.io/ ABBA and dependencies: https://biop.github.io/ijp-imagetoatlas/ FIJI: https://imagej.net/software/fiji/