magellanmapper 1.7a1
3D atlas analysis and annotation
Requires Python: >=3.10

# MagellanMapper

MagellanMapper is a graphical imaging informatics suite for 3D reconstruction and automated analysis of whole specimens and atlases. Its design philosophy is to make the raw 3D images as accessible as possible, simplify annotation from nuclei to atlases, and scale from the laptop or desktop to the cloud in cross-platform environments.

![ROI Editor and Atlas Editor screenshots](https://user-images.githubusercontent.com/1258953/195321971-955fc46a-f44d-4282-8c78-21708ebaeef1.png)

<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781073/"><img align="right" width="200" src="https://user-images.githubusercontent.com/1258953/179440433-0326c4d5-9a9b-4bae-92c7-d09416375bc5.png" title="Current Protocols cover image"></a>


## Quick Reference

- [Docs are now on ReadTheDocs!](https://magellanmapper.readthedocs.io/en/latest/)
- **NEW**: [Vignette of pipelines](bin/sample_cmds_bash.ipynb)
- [Installation](#quick-install) (more [details](docs/install.md))
- [Intro to running MagellanMapper](#run-magellanmapper)
- [Using the viewers](docs/viewers.md)
- [Command-line interface](docs/cli.md)
- [Configuration and settings](docs/settings.md)
- [Publications](#related-publications-and-datasets)


## Quick Install

Install MagellanMapper with its graphical interface and registration tools:

```shell
pip install "magellanmapper[most]"
```

Then launch MagellanMapper:

```shell
mm
```

## Conda Install

Alternatively, [Conda](https://docs.conda.io/en/latest/miniconda.html) can be used to install MagellanMapper:

```shell
conda env create -n mag -f https://raw.githubusercontent.com/sanderslab/magellanmapper/master/envs/environment_rel.yml
```

Then activate the environment (`mag`) and run MagellanMapper:

```shell
conda activate mag
mm
```

## Developer (or "latest and greatest") Install

For the latest updates and fixes, download from Git and install:

```shell
git clone https://github.com/sanderslab/magellanmapper.git
conda env create -n mag -f magellanmapper/environment.yml
mm
```

Or for Pip, replace the `conda` line with:

```shell
pip install -e "magellanmapper[most]"
```

*UPDATE*: As of MM v1.7-pre, Java/Bioformats and a custom Python repo are no longer required to import image files. TIF files can be imported directly into MM.

See the [install docs](docs/install.md) for more details and other install scenarios.

## Using MagellanMapper

MagellanMapper consists of a graphical user interface (GUI), command-line interface (CLI), and application programming interface (API) for Python programmatic access. See the [GUI docs](docs/viewers.md) for graphical usage and the [CLI docs](docs/cli.md) for scripting.

For automated tasks, see the [`sample_cmds_bash.ipynb`](bin/sample_cmds_bash.ipynb) Jupyter Notebook (or the older [`sample_cmds.sh`](bin/sample_cmds.sh) script) that shows examples of running the CLI and exploring images in the GUI. See ReadTheDocs for more details, including [viewer shortcuts](docs/viewers.md) and customizing [settings](docs/settings.md) for your image analysis.

Have a question? Found a bug? Want a feature? Please [ask](https://github.com/sanderslab/magellanmapper/issues)!

### Image file import

MagellanMapper reads large images using on-the-fly loading to reduce memory requirements and load time. NumPy (`.npy`) is the default image format.

Large TIF files can also be opened. In the "Import" tab, you can select files, view and update metadata, and import these files. Proprietary microscopy formats such as CZI can separately converted to TIF in ImageJ/FIJI or the microscope's software. 

Medical imaging formats such as `.mha` (or `.mhd/.raw`) and `.nii` (or `.nii.gz`) can also be opened. 

### Sample 3D data

To try out functions with sample images, download any of these files:

- [Sample region of nuclei at 4x (`sample_region.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/sample_region.zip)
- [Sample downsampled tissue cleared whole brain (`sample_brain.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/sample_brain.zip)
- [Allen Developing Mouse Brain Atlas E18.5 (`ADMBA-E18pt5.zip`)](https://github.com/sanderslab/magellanmapper/releases/download/v1.1.3/ADMBA-E18pt5.zip)

## Related publications and datasets

- For more information on the methods used for 3D atlas construction, please see: https://elifesciences.org/articles/61408
- For step-by-step instructions on using v1.3.x of the software, please see: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpns.104 (now [open access on PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781073/)!); see [ReadTheDocs](https://magellanmapper.readthedocs.io/en/latest/) for ongoing updates
- The 3D reconstructed versions of the Allen Developing Mouse Brain Atlas: https://search.kg.ebrains.eu/instances/Project/b8a8e2d3-4787-45f2-b010-589948c33f20
- Sample wild-type whole mouse brains at age P0: https://search.kg.ebrains.eu/instances/Dataset/2423e103-35e9-40cf-ab0c-0e3d08d24d5a

Licensed under the open-source [BSD-3 license](LICENSE.txt)

Author: David Young, 2017, 2025