CoperniFUS documentation¶

CoperniFUS: A flexible Python-based GUI for stereotaxic experiment planning.

Key features¶

BrainGlobe + Structure highlighting¶

Supports a large range of Brain Atlases and associated structures thanks to BrainGlobe Atlas API.

Stereotaxic frame module - Armature inheritance¶

Arbitrary stereotaxic frames can be easily modelled using a flexible dictionary-based editor.

Stereotaxic frame elements (referred to as Armatures) can be associated in a hierarchical tree structure, allowing operations such as mesh boolean operations or acoustic simulations to be performed in any spatial reference frame.

Anatomical calibration module¶

3D objects can inherit from a anatomically calibrated coordinate frame whose scale and orientation can be simply matched to experimental conditions using anatomical landmarks such as Lambda and Bregma for rodents.

Trimesh boolean operations¶

Integration with the Python library trimesh allows for the manipulation of meshes. This feature greatly simplifies the definition of complex domains in the context of acoustic simulations.

k-Wave acoustic simulation¶

Supports axisymmetric simulations in homogeneous domains and 3D simulations in complex mediums derived from mesh objects.

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.

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