Install

NAVis currently requires Python 3.8 or later. Below instructions assume that you have already installed Python and its package manager pip.

By the way

You can use NAVis without having to install anything on your local machine! Follow this link to open an example notebook in Google’s Colaboratory.

From pip, with “batteries included”

Install navis including optional dependencies plus a GUI backend for the terminal (see bottom of the page for details):

pip3 install navis[all] -U

From pip, as minimal install

On certain systems/setups (e.g. on the new M1 Macs with ARM CPU architecture) you might run into issues during the full install. In that case you can try installing a “minimal” version by dropping the [all]:

pip3 install navis -U

Please see below for a list of the dropped optional dependencies in case you want to try installing them manually!

Development branch from Github

To install the most recent development branch from Github:

pip3 install git+https://github.com/navis-org/navis@master

Optional Dependencies

If you installed navis using pip, mandatory dependencies will have been installed automatically. Unless you used the “batteries included” [all] option, there are a few optional dependencies that e.g. provide speed-boosts in certain situations or are required only for certain functions.

These extras can be installed directly, or along with navis with

pip3 install navis[extra1,extra2]

The user-facing extras, the dependencies they install, and how to install those dependencies directly, are below.

kdtree: pykdtree

Faster than scipy’s cKDTree implementation. If available, will be used to speed up e.g. NBLAST. Important: on Linux I found that I need to set a OMP_NUM_THREADS=4 environment variable (see also pykdtree docs). Otherwise it’s actually slower than scipy’s KDTree.

pip3 install pykdtree

pathos: pathos

Pathos is a multiprocessing library. NAVis uses it to parallelize functions across lists of neurons.

pip3 install pathos

octree: PyOctree

Slower alternative to ncollpyde.

pip3 install pyoctree

r: Rpy2 (rpy2)

Provides interface with R. This allows you to use e.g. the natverse R packages. Note that this package is not installed automatically as it would fail if R is not already installed on the system. You have to install Rpy2 manually!

pip3 install rpy2

shapely: Shapely (shapely)

This is used to get 2D outlines of navis.Volumes.

pip3 install shapely

vispy-* backends: vispy

For 3D visualisation.

Vispy provides a high-performance viewer for 3D visualisation of neurons. Vispy itself has a choice of backends: the one which works for you will depend on your operating system, hardware, other installed packages, and how you’re using navis. The default, supplied with navis’ vispy-default extra, is pyside6; this works best when called from an ipython console. Each of vispy’s backends, listed here, can be installed through vispy and its extras, or navis’ vispy-* extras.

pip3 install navis[vispy-pyqt5]
# or
pip3 install vispy[pyqt5]

hash: xxhash

For speeding up some lookup tables.

flybrains: flybrains

Transforming data between some template Drosophila brains.

cloudvolume: cloud-volume

Reading and writing images, meshes, and skeletons in Neuroglancer precomputed format. This is required required for e.g. the MICrONs interface.

meshes: open3d, pyfqmr

Assorted functionality associated with meshes. pyfqmr in particular is highly recommended if you want to downsample meshes.