PFIA - Pipeline for Image Analysis of Cell Density in Mouse Brain Sections - Test Image Files and Associated Scripts

This dataset contains microscopy image files (".lif"), ImageJ Macro scripts (".ijm"), and R-programming language scripts (".R") associated with the methods article "A framework for systematic, open-science, and user-friendly fluorescence microscopy for reproducible quantification of cells in mouse brain sections" by Sanchez-Arias, Carrier et al., 2021 (under review; this description will be updated if the work is accepted for publication or uploaded to a preprint server). In this work, we review and discussed experimental design and image acquisition and analysis standards for reproducible and open science research. We also provide a FIJI-ImageJ -based systematic workflow to analyze mouse coronal brain section images that includes extracting and storing metadata, exporting and organizing files, and semi-automated registration and cell density analysis. A GitHub repository with the script files is available at https://github.com/SwayneLab/PFIA/ for pull requests, forks, and most up-to-date versions of the scripts. License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.