As a group we are fully committed to open-source and we try very hard to make tools developed in the lab available to the wider community. Please see below list for a summary of the most relevant libraries and don’t hesitate do get in touch either via email or on Github if you have any question or would like to contribute.
R
Libraries for neuron analyses in R are bundled in the natverse suite developed together with the Jefferis lab at the MRC LMB (see also the natverse paper). This includes among others:
- nat is the well-established core library for analysis and visualisation of neuron anatomy
- nat.nblast implements the NBLAST algorithm (Costa et al. 2016) for quantitative comparison of neurons
- rcatmaid provides an interface with CATMAID servers hosting connectomics data
- neuprintr provides an interfaces with neuPrint servers (such as those hosting the Janelia hemibrain connectome)
- nat.flybrains, nat.templatebrains and elmr transform of data from one brain space intro another thus enabling across-dataset comparisons
- fafbseg is a collection of tools to work with the FAFB EM image dataset including the segmentation by FlyWire
Python
For Python, we have developed various libraries mirroring the functionality of above R packages:
- navis is a general purpose library for neuron analysis. It also implements NBLAST, transforms and interfaces with various external tools (NEURON, Blender and the R tools)
- pymaid provides an interfaces with CATMAID server (e.g. those from the Virtual Fly Brain hosting published Drosophila Connectomics data)
- flybrains packages various transforms to move data between brain spaces (thus allowing across-dataset comparisons of e.g. neuron anatomy)
- fafbseg-py is a collection of tools to work with the FAFB EM image dataset including the segmentation by FlyWire
- skeletor is a library for extracting skeletons from 3D meshes
