ArticleCell2021
Whole-body integration of gene expression and single-cell morphology.
Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Perspective on Scanning Electrochemical Probe Microscopy in Single-Cell Imaging.Chemical & biomedical imaging · 2026Review
- A pilot study for whole proteome tagging ineLife · 2026Article
- A pilot study for whole proteome tagging inbioRxiv : the preprint server for biology · 2026Article
- Synthetic data enables human-grade microtubule analysis with foundation models for segmentation.PLoS computational biology · 2026Article
- 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
- Artificial intelligence-powered microscopy: Transforming the landscape of parasitology.Journal of microscopy · 2026Review
- Cellular Hallmarks From Volume Electron Microscopy Reveal Developmental Progression of Plasmodium Ookinetes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- From cells to pixels: A decision tree for designing bioimage analysis pipelines.Journal of microscopy · 2025Article
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- A workflow for semi-automated volume correlative light microscopy and transmission electron tomography.Journal of microscopy · 2025Article
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- In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins.Nature communications · 2025Article
- RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset.PLoS computational biology · 2025Article
- A computational pipeline for spatial mechano-transcriptomics.Nature methods · 2025Article
- Segment Anything for Microscopy.Nature methods · 2025Article
- Single-cell Technology in Stem Cell Research.Current stem cell research & therapy · 2025Review
- Alk1/Endoglin signaling restricts vein cell size increases in response to hemodynamic cues.Angiogenesis · 2024Article
- VI-VS: calibrated identification of feature dependencies in single-cell multiomics.Genome biology · 2024Article
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Animal bodies are composed of cell types with unique expression programs that implement their distinct locations, shapes, structures, and functions. Based on these properties, cell types assemble into specific tissues and organs. To systematically explore the link between cell-type-specific gene expression and morphology, we registered an expression atlas to a whole-body electron microscopy volume of the nereid Platynereis dumerilii. Automated segmentation of cells and nuclei identifies major cell classes and establishes a link between gene activation, chromatin topography, and nuclear size. Clustering of segmented cells according to gene expression reveals spatially coherent tissues. In the brain, genetically defined groups of neurons match ganglionic nuclei with coherent projections. Besides interneurons, we uncover sensory-neurosecretory cells in the nereid mushroom bodies, which thus qualify as sensory organs. They furthermore resemble the vertebrate telencephalon by molecular anatomy. We provide an integrated browser as a Fiji plugin for remote exploration of all available multimodal datasets.
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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.