RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations

Jingpeng Wu, Nicholas Turner, J. Alexander Bae, Ashwin Vishwanathan, H. Sebastian Seung

Research output: Contribution to journalArticlepeer-review

Abstract

Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets.

Original languageEnglish (US)
Article number828169
JournalFrontiers in Neuroinformatics
Volume16
DOIs
StatePublished - Mar 2 2022

All Science Journal Classification (ASJC) codes

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications

Keywords

  • Julia language
  • clustering
  • connectomics
  • morphological analysis
  • neuron connectivity
  • neuron morphology
  • skeletonization

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