Codebase for "A Foundation Model for Cell Segmentation"
☆177Nov 11, 2025Updated 3 months ago
Alternatives and similar repositories for cellSAM
Users that are interested in cellSAM are comparing it to the libraries listed below
Sorting:
- (NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality …☆157Apr 1, 2024Updated last year
- SciCount is tool focused on counting and classifying of objects in image-like data and scientific images, with training and example datas…☆11Oct 24, 2023Updated 2 years ago
- Segment Anything for Histopathology☆58Oct 8, 2025Updated 4 months ago
- MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics☆16Dec 7, 2025Updated 2 months ago
- Segment Anything for Microscopy☆651Feb 18, 2026Updated last week
- CellViT: Vision Transformers for Precise Cell Segmentation and Classification☆359Jul 23, 2025Updated 7 months ago
- A collection of resources on bioimage analysis and related tools and techniques☆14Apr 28, 2023Updated 2 years ago
- Multiple-choice microscopy pipeline☆147Feb 16, 2026Updated last week
- ilastik plugin for napari☆14Dec 15, 2025Updated 2 months ago
- a generalist algorithm for cellular segmentation with human-in-the-loop capabilities☆2,075Updated this week
- Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging☆89Updated this week
- StarDist - Object Detection with Star-convex Shapes☆1,174Feb 14, 2026Updated 2 weeks ago
- Image reading, metadata management, and image writing for Microscopy images in Python☆114Dec 22, 2025Updated 2 months ago
- The known BioVoxxel Toolbox functions now improved for 2D and 3D images☆20Feb 10, 2026Updated 2 weeks ago
- Spatial Single-Cell Analysis Toolkit☆110Feb 20, 2026Updated last week
- computer vision models for single-cell phenotyping☆88Feb 21, 2026Updated last week
- MiC is an ImageJ plugin to compare segmentation masks☆19Jun 4, 2025Updated 8 months ago
- Transformer-based cell tracking for live-cell microscopy☆124Feb 1, 2026Updated 3 weeks ago
- QuPath extension for Cellsparse☆19May 6, 2025Updated 9 months ago
- End-to-end model for cell segmentation and classification☆23Jan 13, 2025Updated last year
- Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy☆88Jan 14, 2026Updated last month
- Threshold independent detection and localization of diffraction-limited spots.☆38Nov 1, 2022Updated 3 years ago
- ☆214Feb 4, 2026Updated 3 weeks ago
- Interactive visualization of spatial omics data☆76Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Nov 16, 2025Updated 3 months ago
- Python playground for cell-type-specific biology☆12Jan 20, 2026Updated last month
- Image processing tool focusing on biological applications☆14Jul 18, 2025Updated 7 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆47Jul 16, 2024Updated last year
- A python algorithm for tracking cells in 3D deforming organs☆68Nov 13, 2025Updated 3 months ago
- The ImageJ plugin to run deep-learning models☆97Oct 28, 2025Updated 4 months ago
- Cell tracking and segmentation software☆173Feb 11, 2026Updated 2 weeks ago
- An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.☆85Feb 10, 2026Updated 2 weeks ago
- Open source Python library for building bioimage analysis pipelines☆189Updated this week
- Java Image Processing Pipeline (JIPipe) is a graphical batch processing language for the ImageJ ecosystem☆19May 27, 2025Updated 9 months ago
- ImageJ plugin for building figures☆16Sep 13, 2023Updated 2 years ago
- ☆17Dec 7, 2023Updated 2 years ago
- ☆14Jan 25, 2024Updated 2 years ago
- SplineDist: Automated Cell Segmentation with Spline Curves☆70Sep 29, 2024Updated last year
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 2 months ago