ArticleFrontiers in neural circuits2022
Igneous: Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling.
Article in Frontiers in neural circuits, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Eyewire II - A connectomic resource for resolving cell types and circuits of the mouse retina.bioRxiv : the preprint server for biology · 2026Article
- MASCAF: A Cable Model Fitting Pipeline for Topologically Complex Surface Meshes.bioRxiv : the preprint server for biology · 2026Article
- Lrrn-mediated retinal ganglion cell targeting drives visual circuit assembly for brightness and contrast detection.Science advances · 2026Article
- PyReconstruct: A fully open-source, collaborative successor to Reconstruct.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Synchrotron Radiation-Based Tomography of an Entire Mouse Brain with Sub-Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Structural Diversity of Mitochondria in the Neuromuscular System across Development Revealed by 3D Electron Microscopy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Ischemic Conditioning Promotes Transneuronal Survival and Stroke Recovery via CD36-Mediated Efferocytosis.Circulation research · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
Three-dimensional electron microscopy images of brain tissue and their dense segmentations are now petascale and growing. These volumes require the mass production of dense segmentation-derived neuron skeletons, multi-resolution meshes, image hierarchies (for both modalities) for visualization and analysis, and tools to manage the large amount of data. However, open tools for large-scale meshing, skeletonization, and data management have been missing. Igneous is a Python-based distributed computing framework that enables economical meshing, skeletonization, image hierarchy creation, and data management using cloud or cluster computing that has been proven to scale horizontally. We sketch Igneous's computing framework, show how to use it, and characterize its performance and data storage.
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Registered trials
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