Usage

As a standalone software

After activation of the coperniFUS_env environment, a standalone coperniFUS instance can be lauched by typing coperniFUS in a terminal (for macOS and linux) or command prompt in Windows.

Assets (such as .stl mesh files) loaded by armatures need to be located in a single directory. By default, example data will be loaded from coperniFUS/examples/assets however this behaviour can be changed by providing an --assets_dir_path argument.

coperniFUS --assets_dir_path 'path/to/your/armature/assets'

Interactively in a notebook

CoperniFUS in interactive mode

General Application Structure

CoperniFUS is architectured around three main components:

  • the Viewer hosting the 3D viewport and all UI elements

  • Modules which allow the manipulation of data displayed in the viewport

  • and Armatures which are submodules lying in the Stereotaxic Frame module and allow the user to conduct operations in the spatial coordinate frames of a stereotaxic aparatus.

../_images/CoperniFUS_ui_breakdown.png

Description of data fields can be obtained by hovering gui elements.

../_images/pointer_tooltip_doc.png

Affine transformations from strings syntax

Throughtout the sofware - in the GUI or configuration dictionaries - transformations of 3D objects can be defined by the user as strings.

The syntax supports:

  • Translation

    • Tx50um (translate 50 micrometers along \(x\))

  • Rotate:

    • Rz12deg (12 degree rotation around \(z\) axis)

  • Scale

    • S0.2 (apply a 0.2 scaling ratio in all directions)

    • Sy30 (apply a 30 scaling ratio along \(y\))

Detailed information of the app structure can be found in the API reference page