ArticleNature communications2024
Petascale pipeline for precise alignment of images from serial section electron microscopy.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 32 citations in OpenAlex.
- Synaptic Organization of the Primate Retina: Toward a Human Foveal Connectome.Annual review of vision science · 2026Review
- Hippocampal CA3 connectomics reveals a gradient of mossy fiber inputs and selective feedforward inhibition onto pyramidal cells.Nature neuroscience · 2026Article
- Article
- 3D registration-guided deformable residual inpainting for ssEM restoration.Bioinformatics (Oxford, England) · 2026Article
- vEMRec: High-Resolution Volume Electron Microscopy Reconstruction Based on Structure-Preserving and High-Fidelity 3D Alignment.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Synaptic-resolution connectomics: towards large brains and connectomic screening.Nature reviews. Neuroscience · 2026Review
- Connectome of a human foveal retina.bioRxiv : the preprint server for biology · 2026Article
- PyReconstruct: A fully open-source, collaborative successor to Reconstruct.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex.Nature neuroscience · 2025Article
- Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Article
- Neuronal wiring diagram of an adult brain.Nature · 2024Article
- Local-Peak Scale-Invariant Feature Transform for Fast and Random Image Stitching.Sensors (Basel, Switzerland) · 2024Article
- Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy.Nature communications · 2024Article
- Article
- FAST-EM array tomography: a workflow for multibeam volume electron microscopy.Methods in microscopy · 2024Article
- Array tomography: trails to discovery.Methods in microscopy · 2024Article
- vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy.GigaScience · 2024Article
- Neuronal wiring diagram of an adult brain.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.