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.

Quick Reference

• Docs are now on ReadTheDocs!
• NEW: Vignette of pipelines
• Installation (more details)
• Intro to running MagellanMapper
• Using the viewers
• Command-line interface
• Configuration and settings
• Publications

Quick Install

Install MagellanMapper with its graphical interface and registration tools:

pip install "magellanmapper[gui,itk]"

Then launch MagellanMapper:

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Conda Install

MagellanMapper can also be installed in Conda:

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:

conda activate mag
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Pre-release

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. To install the latest pre-release in regular or Conda environments, run:

 pip install --pre "magellanmapper[most]"

Developer Install (ie "the latest and greatest")

For the latest updates and fixes, download from Git and install:

git clone https://github.com/sanderslab/magellanmapper.git
conda env create -n mag -f magellanmapper/environment.yml
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Or for Pip, replace the conda line with:

pip install -e "magellanmapper[most]"

See the install docs 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 for graphical usage and the CLI docs for scripting.

For automated tasks, see the sample_cmds_bash.ipynb Jupyter Notebook (or the older 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 and customizing settings for your image analysis.

Have a question? Found a bug? Want a feature? Please ask!

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)
• Sample downsampled tissue cleared whole brain (sample_brain.zip)
• Allen Developing Mouse Brain Atlas E18.5 (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!); see ReadTheDocs 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

Author: David Young, 2017, 2025