neuroboom

========= neuroboom

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.. image:: https://img.shields.io/pypi/v/neuroboom.svg :target: https://pypi.python.org/pypi/neuroboom

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.. image:: /docs/source/_static/logos/nb_large_landing.png :width: 1200 :class: with-shadow

Neuroboom is a suite of Python 3 tools for analysing neuron reconstructions within Connectomic initiatives. This package is currently designed to operate on neuron recontructions within the CATMAID or Neuprint platforms.

These two different platforms reflect the two available connectomic efforts in the fruit fly, Drosophila melanogaster:

1. the Full Adult Female Brain (FAFB) <https://www.sciencedirect.com/science/article/pii/S0092867418307876?via%3Dihub>_ Zheng et al., 2018, Cell
2. the Hemibrain <https://elifesciences.org/articles/57443>_, Scheffer et al., 2020, eLife

Have I seen this before?

Some code incorporated within the neuroboom package has been presented in scientific papers, most notably the dendrogram functions:

1. Integration of Parallel Opposing Memories Underlies Memory Extinction <https://www.sciencedirect.com/science/article/pii/S0092867418310377?via%3Dihub>_, J. Felsenberg et al., 2018, Cell
2. Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila <https://www.cell.com/current-biology/fulltext/S0960-9822(20)30764-8>_, N. Otto, MW Pleijzier et al., 2018, Current Biology
3. Convergence of distinct subpopulations of mechanosensory neurons onto a neural circuit that elicits grooming <https://www.biorxiv.org/content/10.1101/2020.06.08.141341v1>_, S. Hampel et al., 2020, biorXiv

Documentation

• neuroboom is on readthedocs

Features

• Dendrograms: 2D graph representations of neurons.
  • Available in static renderings for scientific papers / representations
  • Interactive renderings for exploratory analyses

Coming soon:

• synaptic focalisation
• electrotonic modelling