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.
General
We develop and maintain https://coda.science – a browser-based, node editor for querying and analyzing connectomic data.
- node-based editor for building analysis/exploration pipelines
- morphological (NBLAST, axon-dendrite splits, etc) and connectivity (graph, shortest path, influence score, etc) analyses
- works with neuPrint, CAVE and CATMAID datasets
- download/export results as CSV, SWC, images, Neuroglancer URLs, etc.
- convert workflows to Python or R code to run locally
- AI assistant for generating workflows from natural language queries
- share workflows via links
Source code on Github.
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
- coconat and coconatfly are libraries for comparative connectomics; the latter is implements a high-level interface for Drosophila datasets
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
- cocoa is a library for comparative connectomics with a focus on Drosophila datasets
- bigclust is a graphical library for interactive exploration and annotation of large (100k’s) hierarchical clusterings
- skeletor implements are range of different methods for extracting skeletons from 3D meshes