ArticleThe Journal of cell biology2023
Deep neural network automated segmentation of cellular structures in volume electron microscopy.
Article in The Journal of cell biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- SIGMA: SIgnaling via Golgi Morphology Analysis for pathway-state classification.bioRxiv : the preprint server for biology · 2026Article
- Presynaptic Vesicles Supply Membrane for Axonal Bouton Enlargement during Long Term Potentiation.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Cell Structure Segmentation in TEM Images of Murine Skin Melanoma Cells by Deep Learning Model.Journal of imaging · 2026Article
- Naked antisense oligonucleotides remain endolysosomally sequestered despite induced membrane damage.bioRxiv : the preprint server for biology · 2026Article
- Synthetic data enables human-grade microtubule analysis with foundation models for segmentation.PLoS computational biology · 2026Article
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- CabioRxiv : the preprint server for biology · 2026Article
- Leveraging AI for cell biology discovery.Biochemical Society transactions · 2026Review
- Close-up of vesicular ER exit sites by volume electron imaging using FIB-SEM.The Journal of cell biology · 2026Article
- Cellular Hallmarks From Volume Electron Microscopy Reveal Developmental Progression of Plasmodium Ookinetes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tau seeding in neurons enabled by transient endolysosomal perforations are confined within endolysosomes.bioRxiv : the preprint server for biology · 2025Article
- AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact.The Journal of cell biology · 2025Article
- DeepSCEM: A User-Friendly Solution for Deep Learning-Based Image Segmentation in Cellular Electron Microscopy.Biology of the cell · 2025Article
- DeepEM Playground: Bringing deep learning to electron microscopy labs.Journal of microscopy · 2025Article
- Segment Anything for Microscopy.Nature methods · 2025Article
- Neuronal constitutive endolysosomal perforations enable α-synuclein aggregation by internalized PFFs.The Journal of cell biology · 2025Article
- Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.Nature protocols · 2024Review
- Electron Microscopy Techniques for 3D Plant ER Imaging.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Constitutive Endolysosomal Perforation in Neurons allows Induction of α-Synuclein Aggregation by Internalized Pre-Formed Fibrils.bioRxiv : the preprint server for biology · 2024Article
- Plantorganelle Hunter is an effective deep-learning-based method for plant organelle phenotyping in electron microscopy.Nature plants · 2023Article
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
Volume electron microscopy is an important imaging modality in contemporary cell biology. Identification of intracellular structures is a laborious process limiting the effective use of this potentially powerful tool. We resolved this bottleneck with automated segmentation of intracellular substructures in electron microscopy (ASEM), a new pipeline to train a convolutional neural network to detect structures of a wide range in size and complexity. We obtained dedicated models for each structure based on a small number of sparsely annotated ground truth images from only one or two cells. Model generalization was improved with a rapid, computationally effective strategy to refine a trained model by including a few additional annotations. We identified mitochondria, Golgi apparatus, endoplasmic reticulum, nuclear pore complexes, caveolae, clathrin-coated pits, and vesicles imaged by focused ion beam scanning electron microscopy. We uncovered a wide range of membrane-nuclear pore diameters within a single cell and derived morphological metrics from clathrin-coated pits and vesicles, consistent with the classical constant-growth assembly model.
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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.