ArticleCell reports methods2025
Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.
Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- NucleoNet and DropNet: Generalist deep learning models for instance segmentation of nuclei and lipid droplets from electron microscopy images.bioRxiv : the preprint server for biology · 2026Article
- From Microscopy to Nanoscopy: Contemporary Physical Methods in Mitochondrial Structural Biology.International journal of molecular sciences · 2026Review
- MitoEM 2.0: A Benchmark for Challenging 3D Mitochondria Instance Segmentation from EM Images.bioRxiv : the preprint server for biology · 2025Article
- Investigation of neuromodulation of the endbulb of Held synapse in the cochlear nucleus by serotonin and norepinephrine.Frontiers in cellular neuroscience · 2025Article
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Authors and funding
6 authors.
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Abstract
Recent technical advances in volume electron microscopy (vEM) and artificial-intelligence-assisted image processing have facilitated high-throughput quantifications of cellular structures, such as mitochondria, that are ubiquitous and morphologically diversified. A still often-overlooked computational challenge is to assign a cell identity to numerous mitochondrial instances, for which both mitochondrial and cell membrane contouring used to be required. Here, we present a vEM reconstruction procedure (called mito-SegEM) that utilizes virtual-path-based annotation to assign automatically segmented mitochondrial instances at the cellular scale, therefore bypassing the requirement of membrane contouring. The embedded toolset in webKnossos (an open-source online annotation platform) is optimized for fast annotation, visualization, and proofreading of cellular organelle networks. We demonstrate the broad applications of mito-SegEM on volumetric datasets from various tissues, including the brain, intestine, and testis, to achieve an accurate and efficient reconstruction of mitochondria in a use-dependent fashion.
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