NAVis & friends

navis comes with batteries included but is also highly extensible. Here are some libraries that are built directly on top of navis.

flybrains

flybrains is a package that bundles fly template brains and transforms that navis can use to map spatial data (e.g. neurons) from one brain space to another. If you installed navis via pip with the [all] option, flybrains will already be on your system.

pymaid

pymaid provides an interface with CATMAID servers. It allows you to pull data (neurons, connectivity) that can be directly plugged into navis. Conversely, you can also take navis neurons and push them to a CATMAID server. pymaid is a great example of how to extend navis.

fafbseg

fafbseg contains tools to work with autosegmented data for the FAFB (full adult fly brain) EM dataset. It brings together data from FlyWire, Google’s segmentation of FAFB and synapse predictions by Buhmann et al. (2019).

natverse

The natverse is navis' equivalent in R. While we are aiming for feature parity, it can be useful to access natverse functions from Python. For this, navis offers some convenience functions using the R-Python interface rpy2. Check out the tutorial.