GNN-based cell segmentation of spatial transcriptomics data
☆22Aug 27, 2026Updated this week
Alternatives and similar repositories for segger
Users that are interested in segger are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90May 25, 2026Updated 3 months ago
- ☆31Aug 7, 2026Updated 3 weeks ago
- Profile purification of single-cell spatial transcriptomics data☆54Jun 29, 2026Updated 2 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆80Aug 22, 2026Updated last week
- k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.☆16Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Code for paired TCR data analysis from TIRTL-seq experiments☆14Nov 24, 2025Updated 9 months ago
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆39Jul 7, 2026Updated last month
- ☆17Aug 20, 2026Updated last week
- ☆38Aug 15, 2026Updated 2 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆187Updated this week
- rna2seg☆25May 15, 2025Updated last year
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆155Aug 21, 2026Updated last week
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.☆18Updated this week
- A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless …☆24Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Automatically annotate cell types, consistently across samples.☆27Updated this week
- Configure Vitessce using existing Scverse plotting APIs☆25Aug 7, 2026Updated 3 weeks ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Updated this week
- Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org☆14Updated this week
- Implementation of CellNEST method☆69Jun 23, 2026Updated 2 months ago
- Spatial and multiomic visualization and analysis library☆55Updated this week
- CAST package☆44Oct 26, 2024Updated last year
- Variance stabilizing transformation for Gamma Poisson distributed data☆22Apr 11, 2023Updated 3 years ago
- Repository to perform mapping of new datasets to the Human Lung Cell Atlas.☆20Jun 7, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Efficient data structures and IO for whole slide image analysis☆33Updated this week
- ☆56Aug 12, 2026Updated 2 weeks ago
- ☆12May 29, 2024Updated 2 years ago
- Test genes for Spatial Variation☆15Dec 20, 2024Updated last year
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆291Updated this week
- Single-cell spatial omics analysis that makes you happy!☆72Updated this week
- ☆13Aug 9, 2022Updated 4 years ago
- R/Bioconductor package to interactively explore single cell clusters at multiple resolutions☆12Mar 10, 2022Updated 4 years ago
- ☆38Jan 22, 2026Updated 7 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Multi-Dimensional Visualization (MDV) is an open-source toolkit for analyzing and visualizing spatial and molecular datasets. Code licens…☆38Updated this week
- ☆27Oct 12, 2024Updated last year
- Cross-attention-based cell-cell interaction inference from ST data.☆22Jul 31, 2026Updated 3 weeks ago
- Detect hierarchical structures in cell-cell communications☆16Jan 26, 2025Updated last year
- Single cell omics biology annotations☆61Jul 7, 2026Updated last month
- Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"☆23Dec 1, 2024Updated last year
- ☆13Dec 20, 2025Updated 8 months ago