devAP_histology

This repository is a fork of petersaj/AP_histology, adapted to support both adult and developmental mouse brain atlases.
It has been further modified to integrate smoothly with the related repositories in this GitHub profile:

• 🧠 CELL3D — for processing and visualizing 3D cell coordinate data
  
• 🧠 VOL3D — for plotting and analyzing traced injection volumes in 3D

These tools are designed to work together for comprehensive anatomical reconstruction and analysis.

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Key Adaptations

• Allen Mouse Brain Atlas — pre-processed and included directly through AP_histology, based on Wang Q, et al., 2020 https://doi.org/10.1016/j.cell.2020.04.007)
• Developmental Mouse Brain Atlas (P4–P14) — based on Kronman et al., 2024 (DOI: 10.1038/s41467-024-53254-w)
• Standardized processing of files (redacted some functions from the original APhist, eg scaling of images)
• Large files managed with Git LFS for reliable download and version control

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Requirements

• MATLAB (2020 or later recommended)
• npy-matlab (for reading .npy files)
• Git LFS (see below)

Installation/Cloning of scripts

This repository uses Git Large File Storage (LFS) to manage large atlas files (e.g., .npy atlas files).

🔧 To install Git, go to: https://git-scm.com/downloads and download and install Git for Windows. During installation, keep most default settings. Make sure Git Bash and Git CMD options are enabled.

🔧 You also need to install Git LSF: Go to: https://git-lfs.github.com/, click Download, then install Git LFS with the installer.

Before cloning or pulling this repo, please run the following once in your command prompt (Hit the Windows key, type cmd, and open the Command Prompt): bash git lfs install

This sets up Git LFS for your system. You only need to run this once.

Now you can clone the repository that uses LFS to copy files into your path of choosing:

``` bash

Replace with your own path

cd /path/to/your/folder git clone https://github.com/jkaiser87/devAP_histology.git ```

If you skip git lfs install, you’ll only get placeholder pointer files instead of usable atlas data.

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Atlas Setup

This repository includes the atlases in compressed .zip format to reduce storage load. After cloning, manually unzip the following files:

allenAtlas.zip → unzips to allenAtlas/

devAtlas.zip → unzips to devAtlas/

Make sure both folders are extracted to the root of the repo (same level as README.md), so the pipeline can find them.

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Required Dependency: npy-matlab

This pipeline uses .npy files (NumPy format) for some atlas data.
To read these in MATLAB, you must install the npy-matlab toolbox.

1. Clone or download the repository:

```bash

Recommended: clone into the devAP_histology folder

cd /path/to/devAP_histology git clone https://github.com/kwikteam/npy-matlab.git ``` Alternatively, download and extract it from GitHub manually.

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Add folder to MATLAB Path

After cloning, add the repo and its dependencies to your MATLAB path.

In MATLAB: matlab addpath(genpath('C:\Path\To\devAP_histology')) addpath(genpath('C:\Path\To\npy-matlab')) % if cloned elsewhere savepath

Or, in the MATLAB GUI: Go to Home > Set Path > Add with Subfolders…, select the folder(s), and click Save.

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Running devAP_histology

To run the pipeline with a selected atlas, open MATLAB and call:

matlab AP_histology("P4") % uses the P4 developmental atlas AP_histology("P14") % uses the P14 developmental atlas AP_histology() % defaults to the adult Allen atlas

Note on Developmental Atlas Alignment

The auto-alignment procedure (AP_histology) was originally optimized for adult mouse brains using the Allen CCF. While the same framework has been extended to the developmental atlas (devCCF), automatic alignment often performs less reliably on P4–P14 slices due to differences in brain morphology, lower tissue contrast, and less well-defined landmarks.

• Carefully check alignment outputs
• Use manual adjustments or supplemental landmarks (e.g., bregma points, anatomical ROIs) if needed

Atlas Sources and Credits

Allen Mouse Brain Atlas

Wang Q, et al. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell. DOI: 0.1016/j.cell.2020.04.007

Developmental Mouse Brain Atlas (P4–P14)

Kronman, F.N., et al. (2024).
A Common Coordinate Framework for the Developing Mouse Brain. Nature Communications.
DOI: 10.1038/s41467-024-53254-w

License

This project is released under the MIT License, as inherited from the original AP_histology.