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.