ArticlePLoS computational biology2021
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Golgi organization regulates stem cell function in the small intestine.Nature communications · 2026Article
- CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images.Nature protocols · 2026Review
- Cell Structure Segmentation in TEM Images of Murine Skin Melanoma Cells by Deep Learning Model.Journal of imaging · 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
- Chloroplast Stress Signals Orchestrate Epidermis-Specific Remodeling of Mitochondria and ER Under High Light.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deep learning analysis of particle content in extracted slow-release morphine: longer boiling reduces large fragments while retaining morphine extraction.Scientific reports · 2026Article
- Article
- Systematic evaluation of computational methods for cell segmentation.Briefings in bioinformatics · 2026Article
- Multiscale mitochondrial cristae remodeling links Opa1 downregulation to reduced OXPHOS capacity in aged hearts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A semi-automated algorithm for image analysis of respiratory organoids.PLoS computational biology · 2025Article
- DeepSCEM: A User-Friendly Solution for Deep Learning-Based Image Segmentation in Cellular Electron Microscopy.Biology of the cell · 2025Article
- Nuclear envelope-associated lipid droplets are enriched in cholesteryl esters and increase during inflammatory signaling.The EMBO journal · 2025Article
- Article
- Segment Anything for Microscopy.Nature methods · 2025Article
- AI-based hardware and software tools in microscopy to boost research in immunology and virology.Frontiers in immunology · 2025Review
- Article
- State-of-the-Art Deep Learning Methods for Microscopic Image Segmentation: Applications to Cells, Nuclei, and Tissues.Journal of imaging · 2024Review
- A unique symbiosome in an anaerobic single-celled eukaryote.Nature communications · 2024Article
- Dynamic microvilli sculpt bristles at nanometric scale.Nature communications · 2024Article
- Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.Nature protocols · 2024Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present DeepMIB, a new software package that is capable of training convolutional neural networks for segmentation of multidimensional microscopy datasets on any workstation. We demonstrate its successful application for segmentation of 2D and 3D electron and multicolor light microscopy datasets with isotropic and anisotropic voxels. We distribute DeepMIB as both an open-source multi-platform Matlab code and as compiled standalone application for Windows, MacOS and Linux. It comes in a single package that is simple to install and use as it does not require knowledge of programming. DeepMIB is suitable for everyone interested of bringing a power of deep learning into own image segmentation workflows.
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