Installation and setup

Requirements

This package requires Python >= 3.8.

Basic installation

Assuming you have the correct version of Python installed, you can install neuromaps-mouse by opening a terminal and running the following:

git clone https://github.com/netneurolab/neuromaps-mouse.git
cd neuromaps-mouse
pip install .

Optional dependencies

Some functionality in neuromaps-mouse requires additional dependencies.

Pyvista

Pyvista is the plotting library used in the package for 3D surface visualization. This will allow you to use functions like

neuromaps_mouse.plotting.plot_allenccfv3_3d()

You will need a working Pyvista installation. We recommend using a clean conda environment and installing Pyvista using the following commands:

conda create -n plotting python=3.12
conda activate plotting
conda install -c conda-forge pyvista

Pyvista is actively maintained and generally installs without issues. Please also check out their detailed installation guide.

Pyvista is built on top of VTK, which supports multiple OpenGL window backends and you can choose one that fits your environment (see the VTK runtime settings):

X11: standard Linux display server (requires an active X server)
Win32: native Windows OpenGL context
EGL: offscreen GPU context (good for headless servers with GPUs)
OSMesa: CPU-based software rendering (good for headless servers without GPUs)

For example, on a headless Linux server without a GPU you can request OSMesa by setting the backend before importing PyVista/VTK:

import os
os.environ["VTK_DEFAULT_OPENGL_WINDOW"] = "vtkOSOpenGLRenderWindow"