NEURD offers automated proofreading and feature extraction for connectomics
Abstract
Abstract We are in the era of millimetre-scale electron microscopy volumes collected at nanometre resolution 1,2 . Dense reconstruction of cellular compartments in these electron microscopy volumes has been enabled by recent advances in machine learning 3–6 . Automated segmentation methods produce exceptionally accurate reconstructions of cells, but post hoc proofreading is still required to generate large connectomes that are free of merge and split errors. The elaborate 3D meshes of neurons in these volumes contain detailed morphological information at multiple scales, from the diameter, shape and branching patterns of axons and dendrites, down to the fine-scale structure of dendritic spines. However, extracting these features can require substantial effort to piece together existing tools into custom workflows. Here, building on existing open source software for mesh manipulation, we present Neural Decomposition (NEURD), a software package that decomposes meshed neurons into compact and extensively annotated graph representations. With these feature-rich graphs, we automate a variety of tasks such as state-of-the-art automated proofreading of merge errors, cell classification, spine detection, axonal-dendritic proximities and other annotations. These features enable many downstream analyses of neural morphology and connectivity, making these massive and complex datasets more accessible to neuroscience researchers.
Article Details
Authors (58)
Brendan Celii
Stelios Papadopoulos
Zhuokun Ding
Paul G. Fahey
Eric Wang
Christos Papadopoulos
Alexander B. Kunin
Saumil Patel
J. Alexander Bae
Agnes L. Bodor
Derrick Brittain
JoAnn Buchanan
Daniel J. Bumbarger
Manuel A. Castro
Erick Cobos
Sven Dorkenwald
Leila Elabbady
Akhilesh Halageri
Zhen Jia
Chris Jordan
Dan Kapner
Nico Kemnitz
Sam Kinn
Kisuk Lee
Kai Li
Ran Lu
Thomas Macrina
Gayathri Mahalingam
Eric Mitchell
Shanka Subhra Mondal
Shang Mu
Barak Nehoran
Sergiy Popovych
Casey M. Schneider-Mizell
William Silversmith
Marc Takeno
Russel Torres
Nicholas L. Turner
William Wong
Jingpeng Wu
Szi-chieh Yu
Wenjing Yin
Daniel Xenes
Lindsey M. Kitchell
Patricia K. Rivlin
Victoria A. Rose
Caitlyn A. Bishop
Brock Wester
Emmanouil Froudarakis
Edgar Y. Walker
Fabian Sinz
H. Sebastian Seung
Forrest Collman
Nuno Maçarico da Costa
R. Clay Reid
Xaq Pitkow
Andreas S. Tolias
Jacob Reimer