Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
☆49Jul 16, 2024Updated last year
Alternatives and similar repositories for BIDCell
Users that are interested in BIDCell are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Sub-cellular spatial transcriptomics Cell Segmentation☆70Oct 1, 2023Updated 2 years ago
- ☆53Oct 9, 2025Updated 7 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆171Updated this week
- ☆17Dec 7, 2023Updated 2 years ago
- UNet script, model, sample data☆14Feb 19, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Bayesian Segmentation of Spatial Transcriptomics Data☆205Apr 30, 2026Updated 3 weeks ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆277May 7, 2026Updated 2 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Nov 16, 2025Updated 6 months ago
- ☆38Dec 13, 2023Updated 2 years ago
- ☆46Feb 13, 2026Updated 3 months ago
- End-to-end model for cell segmentation and classification☆22Jan 13, 2025Updated last year
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆96Apr 30, 2026Updated 3 weeks ago
- BANKSY: spatial clustering☆147May 2, 2026Updated 2 weeks ago
- Interactive visualization of spatial omics data☆86May 15, 2026Updated last week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆38Apr 30, 2026Updated 3 weeks ago
- TACCO: Transfer of Annotations to Cells and their COmbinations☆65Apr 21, 2026Updated last month
- Spatial Single Cell Analysis in Python☆571Updated this week
- Profile purification of single-cell spatial transcriptomics data☆44Updated this week
- comseg☆24Feb 6, 2025Updated last year
- Supervised cell type identification for scATAC-seq data☆15Aug 23, 2023Updated 2 years ago
- From geospatial to spatial -omics☆103May 8, 2026Updated last week
- Multi-slice Spatial Transcriptome Domain Analysis.☆13Dec 13, 2024Updated last year
- ☆17Jul 8, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆99Dec 11, 2023Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆173May 8, 2026Updated 2 weeks ago
- ☆31Updated this week
- [PLoS Computational Biology 2025] SpaMask: Dual Masking Graph Autoencoder with Contrastive Learning for Spatial Transcriptomics☆13Apr 8, 2025Updated last year
- We propose SpatialCVGAE, which uses multiple variational graph autoencoders with different initializations to simultaneously generate cor…☆13Jun 24, 2025Updated 10 months ago
- A collection of resources on bioimage analysis and related tools and techniques☆14Apr 28, 2023Updated 3 years ago
- Implementation of multiplex Leiden for analysis of spatial omics data☆18May 7, 2026Updated 2 weeks ago
- An open and interoperable data framework for spatial omics data☆370Updated this week
- ☆60Feb 14, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Automated Cell Toolkit☆24Oct 15, 2025Updated 7 months ago
- Spatial alignment of single cell transcriptomic data.☆365Jul 1, 2025Updated 10 months ago
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- ☆10Jan 17, 2023Updated 3 years ago
- ☆95Updated this week
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆35Jul 24, 2025Updated 9 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90Mar 16, 2026Updated 2 months ago