Tool landscape

Below are brief descriptions of the libraries/packages. For details, I defer to their respective (excellent) documentations.

Querying VFB

Queries against VFB’s REST API are easiest with vfb_connect for Python. For R there is a vfb_connect wrapper, vfbconnectr. See also David’s presentation for details.

R

In R, the natverse is your one-stop-shop for all things neuron: it’s a collection of various R packages that are built on top of the neuroanatomy toolbox, nat. Of particular relevance for this workshop:

1. nat is a general purpose library for working with morphological neuron data. In this workshop, we make heavy use of nat’s plotting capabilities but its capabilities extend far beyond that. If you want to run any morphological analysis, I highly recommend you have a look at the “Articles” in nat’s doc.
2. neuprintr and hemibrainr provide an interface with neuprint and the Janelia hemibrain dataset (link). The former lets you run queries against neuprint’s neo4j database while the latter contains meta data and various convenience functions to work with the hemibrain dataset.
3. rcatmaid provides an interface with CATMAID servers such as those the VFB uses to host published from the FAFB or larval fruit fly dataset. rcatmaid is built on top of nat and you can use nat functions with neurons pulled via rcatmaid.

Python

In Python, we find packages analogous to those in R:

1. navis is nat’s serpentine sibling: a general purpose neuron library for visualization and analysis of neuronal morphologies. It also features interfaces e.g. with Blender 3D and the natverse via rpy2.
2. python-neuprint is a Python library to interface with neuprint maintained by Janelia. Note that navis wraps this library and adds some convenience functions. See this tutorial.
3. pymaid lets you interface with CATMAID servers. Critically, it’s built on top of navis and you can natively use navis functions with pymaid neurons. Note that due to a name clash the library is called python-catmaid on PyPI.

Noteworthy mentions

There are a few more packages/functions that you might hear of over the course of the workshop.

NBLAST

NBLAST is an algorithm that computes morphological similarity between neurons (Costa et al., 2016). This has proven incredibly useful to find similar neurons across datasets but also to cluster neurons into cell types.

On the R side the algorithm is implemented in nat.nblast and in Python it is part of navis (see this tutorial).

Transforms

You will note that neurons pulled from VFB are typically in the same template space which makes co-visualization of neurons from different datasets a breeze. If you want to transform spatial data between template brains, e.g. from FAFB (“FAFB14”) to hemibrain (“JRCFIB2018F”), you should look for nat.flybrains & nat.jrcbrains in R and navis-flybrains in Python.