Morphology Suite

NeuroM

Blue Brain NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.

Neuron morphologies are tightly coupled to neuron electrical properties and therefore are a crucial part of understanding the neuron as a functional unit.

The NeuroM software has been designed to enable researchers to quickly pinpoint the characteristics and specificities of every neuron.

It is composed of a low-level API for reading morphology files on top of which are built several applications: a morphology file validator, a feature extractor and a morphology viewer.

This software is used in use cases in the EBRAINS Cellular Level Simulation Platform.

Blue Brain NeuroTS

Blue Brain NeuroTS is a tool that generates, i.e., synthesizes, digital neuronal morphologies, based on the topological profiles of different cell types.

NeuroTS is distributed as a Python package and uses morphological reconstructions of Neurolucida ASCII files, H5 or SWC as input to extract input distributions, based on the python libraries for analyzing morphologies  Blue Brain NeuroM and  Blue Brain TMD.

NeuroTS uses the input distributions that were extracted from the original neuronal reconstructions to generate digital version of neuronal morphologies. The synthesized morphologies are statistically similar to the original reconstructions.

NeuroMorphoVis

Blue Brain’s NeuroMorphoVis is an interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks.

NeuroMorphoVis is based on Blender, but it does not require knowledge of Blender. The source code and documentation are available under the GNU public license on Github.

Blue Brain NeuroR

Blue Brain NeuroR is a collection of tools to repair morphologies.

NeuroR is distributed as a Python package and uses our python library for analyzing morphologies Blue Brain NeuroM.

There are three types of morphology repair with NeuroR: Sanitization – the process ofcurating a morphological file, Cut plane repair – which aims at regrowing parts of morphologies that have been cut out when the cell has been experimentally sliced and Unravelling – the action of “stretching” the cell that has been shrunk because of the dehydration caused by the slicing.

Morphology Workflows

This project contains several workflows for processing morphologies:

  • Fetch: download morphologies from online database (like Allen, NeuroMorpho or MouseLight).
  • Placeholders: compute the place holders for a given region and mtype set.
  • Curate: from raw morphologies, ensures that morphologies can be used with the rest of BBP codes. 
  • Annotate: create various annotations on morphologies needed by specific BBP codes. 
  • Repair: process morphologies to correct for artifacts of in-vitro reconstruction.