Package: magellanmapper
MagellanMapperMagellanMapper 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 ReferenceNEW:Docs are now on ReadTheDocs!Installation(moredetails)Intro to running MagellanMapperUsing the viewersCommand-line interfaceConfiguration and settingsPublicationsInstallationIf you use Conda (availablehere), you can install MagellanMapper into a new environment:condaenvcreate-nmag-fhttps://raw.githubusercontent.com/sanderslab/magellanmapper/master/envs/environment_rel.ymlTo run in this new environment namedmag*:condaactivatemag
mm*mmwas added in v1.6.0 to launch from installed packagesOr install using Pip (virtual environmentrecommended):pipinstall"magellanmapper[most]"--extra-index-urlhttps://pypi.fury.io/dd8/The extra index accesses a fewcustomized dependenciesfor MagellanMapper.Conda installs Java to import proprietary image file formats, which can also be installed separately when using Pip (eg fromhere).For the latest updates and fixes, download from Git and install:gitclonehttps://github.com/sanderslab/magellanmapper.git
condaenvcreate-nmag-fenvironment.yml
pipinstall-e".[most]"--extra-index-urlhttps://pypi.fury.io/dd8/
pythonrun.pyOr for Pip, replace"magellanmapper[most]"with".[most]".More ways to install and runSee theinstall docsfor more details, including:Installer scripts, which install Miniconda and MagellanMapper without requiring command-line usageInstaller packages, for point-and-click installationUsing MagellanMapperMagellanMapper consists of a graphical user interface (GUI), command-line interface (CLI), and application programming interface (API) for Python programmatic access. See theGUI docsfor graphical usage and theCLI docsfor scripting.For automated tasks, see thesample_cmds_bash.ipynbJupyter Notebook (or the oldersample_cmds.shscript) that shows examples of running the CLI and exploring images in the GUI. See ReadTheDocs for more details, includingviewer shortcutsand customizingsettingsfor your image analysis.Have a question? Found a bug? Want a feature? Pleaseask!Image file importLarge images or proprietary microscopy formats such as CZI can be imported by MagellanMapper into NumPy format, which allows on-the-fly loading to reduce memory requirements and initial loading time. In the "Import" tab, you can select files, view and update metadata, and import the files.Medical imaging formats such as.mha(or.mhd/.raw) and.nii(or.nii.gz) can be opened with the SimpleITK/SimpleElastix library and do not require separate import.Sample 3D dataTo 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 datasetsFor more information on the methods used for 3D atlas construction, please see:https://elifesciences.org/articles/61408For 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(nowopen access on PubMed!); seeReadTheDocsfor ongoing updatesThe 3D reconstructed versions of the Allen Developing Mouse Brain Atlas:https://search.kg.ebrains.eu/instances/Project/b8a8e2d3-4787-45f2-b010-589948c33f20Sample wild-type whole mouse brains at age P0:https://search.kg.ebrains.eu/instances/Dataset/2423e103-35e9-40cf-ab0c-0e3d08d24d5aLicensed under the open-sourceBSD-3 licenseAuthor: David Young, 2017, 2023, Stephan Sanders Lab