ArticleeLife2021
Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Partaker: deep-learning-based single-cell-resolution analysis of multi-dimensional, long-term, microfluidic-based time-lapse microscopy data.Bioinformatics (Oxford, England) · 2026Article
- Artificial Intelligence-Empowered Single-Cell Phenotyping for Rapid, Automated Pathogen Diagnostics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Phenotypic heterogeneity optimizes trade-offs during adaptive deployment of the type VI secretion system.PLoS biology · 2026Article
- Deep-learning deconvolution and segmentation of fluorescent membranes for high-precision bacterial cell-size profiling.Communications biology · 2026Article
- Biofilms: from the cradle of life to life support.NPJ biofilms and microbiomes · 2026Review
- Article
- Virus Propagation Linked to Exceedingly Rare Gene-Expression Errors: A Single-Molecule Microscopy Demonstration.ACS chemical biology · 2025Article
- Attention-driven UNet enhancement for accurate segmentation of bacterial spore outgrowth in microscopy images.Scientific reports · 2025Article
- Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells.PLoS computational biology · 2025Article
- Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images.PLoS computational biology · 2025Article
- Optimizing TB Bacteria Detection Efficiency: Utilizing RetinaNet-Based Preprocessing Techniques for Small Image Patch Classification.International journal of biomedical imaging · 2025Article
- Light-dependent modulation of protein localization and function in living bacteria cells.Nature communications · 2024Article
- Emergence of bacterial glass.PNAS nexus · 2024Article
- Article
- Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges.ACS omega · 2024Review
- Tools and methods for high-throughput single-cell imaging with the mother machine.bioRxiv : the preprint server for biology · 2024Article
- Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy.PLoS computational biology · 2023Article
- Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker.PLoS computational biology · 2023Article
- Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria.Nature communications · 2023Article
- Phage-antibiotic synergy: Cell filamentation is a key driver of successful phage predation.PLoS pathogens · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based 2D segmentation method that automatically segments single bacteria in complex images of interacting bacterial communities with very little parameter adjustment, independent of the microscopy settings and imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.
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Registered trials
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