Load MagellanMapper and Image Files

Start MagellanMapper

Once you’ve installed MagellanMapper, activate its environment and launch the app:

conda activate mag
mm

Replace the conda command if you are using another type of virtual environment.

The graphical user interface (GUI) should open, allowing you to load images using the browsing controls.

Import images

Importing image files allows them to be read on-the-fly for lower memory requirements. The “Import” panel in the GUI allows you to select files to import, specify metadata, and load them into a NumPy (NPY) format.

TODO: add details

Load TIF files directly

v1.6 added EXPERIMENTAL support for loading TIF images similarly to NPY images but without requiring prior import. Loading a .tif file in the “ROI > Image path” controls will attempt to load the image directly.

Using the CLI

See our Jupyter Notebook for examples of loading and viewing various types of images in MagellanMapper using the command-line interface (CLI).