scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
☆106Mar 1, 2026Updated this week
Alternatives and similar repositories for scPortrait
Users that are interested in scPortrait are comparing it to the libraries listed below
Sorting:
- Automatically annotate cell types, consistently across samples.☆19Feb 23, 2026Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆39Feb 8, 2026Updated 3 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Nov 16, 2025Updated 3 months ago
- Registry for scverse ecosystem packages☆34Updated this week
- An open and interoperable data framework for spatial omics data☆351Feb 24, 2026Updated last week
- Interactive visualization of spatial omics data☆76Feb 24, 2026Updated last week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆263Feb 24, 2026Updated last week
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated 8 months ago
- Single-cell spatial omics analysis that makes you happy!☆52Updated this week
- Slides and Notebooks for scverse 2024☆17Sep 24, 2024Updated last year
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆60Updated this week
- Package for the analysis of Transcripts outside segmented cells in ST data☆26Feb 23, 2026Updated last week
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 2 months ago
- Framework for image and flow cytometry analysis☆32Jan 3, 2026Updated 2 months ago
- Build contrasts for models defined with formulaic☆12Feb 23, 2026Updated last week
- ☆89Updated this week
- ☆14Feb 24, 2026Updated last week
- Static plotting for spatialdata☆74Updated this week
- Spatial Single-Cell Analysis Toolkit☆110Feb 20, 2026Updated last week
- rapids_singlecell: GPU-accelerated framework for scRNA analysis☆300Feb 23, 2026Updated last week
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated last month
- Self-Supervised Vision Transformers for multiplexed imaging datasets☆60Jul 1, 2024Updated last year
- Python API and Jupyter widget for Vitessce☆62Feb 12, 2026Updated 2 weeks ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆119Feb 24, 2026Updated last week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆86Jan 19, 2026Updated last month
- Multimodal Data (.h5mu) implementation for Python☆109Feb 23, 2026Updated last week
- Bayesian Segmentation of Spatial Transcriptomics Data☆202Dec 10, 2024Updated last year
- Single-cell perturbation analysis☆289Feb 23, 2026Updated last week
- R API and htmlwidget for Vitessce☆44Aug 13, 2025Updated 6 months ago
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆25Apr 8, 2025Updated 10 months ago
- Test genes for Spatial Variation☆183May 7, 2024Updated last year
- GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems☆38Jul 11, 2025Updated 7 months ago
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- From geospatial to spatial -omics☆100Feb 12, 2026Updated 2 weeks ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆76Nov 2, 2025Updated 4 months ago
- Cookiecutter template for scverse☆88Feb 23, 2026Updated last week
- Multi-omic single-cell optimal transport tools☆190Feb 23, 2026Updated last week
- CAST package☆42Oct 26, 2024Updated last year