labsyspharm / scimap
Spatial Single-Cell Analysis Toolkit
☆86Updated last month
Alternatives and similar repositories for scimap:
Users that are interested in scimap are comparing it to the libraries listed below
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆33Updated 10 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆109Updated last week
- ☆28Updated 3 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆76Updated 2 weeks ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 9 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆23Updated this week
- Histology Topography Cytometry Analysis Toolbox☆67Updated last year
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆75Updated last year
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆47Updated last month
- Integrated pipeline for multiplexed image analysis☆82Updated this week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆170Updated this week
- Interactive visualization of spatial omics data☆51Updated this week
- Super-resolved spatial transcriptomics by deep data fusion☆71Updated last year
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆56Updated 4 months ago
- ☆27Updated 5 months ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆35Updated last year
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆45Updated 2 years ago
- ☆41Updated 3 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆40Updated 7 months ago
- ☆34Updated 11 months ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆56Updated this week
- Interoperability between SpatialData and the Xenium Explorer☆19Updated 7 months ago
- ☆51Updated last week
- ☆31Updated 2 months ago
- ☆49Updated 9 months ago
- Code used to benchmark Xenium☆45Updated 8 months ago
- Join subcellular Visium HD bins into cells☆85Updated 3 months ago
- Multiple-choice microscopy pipeline☆123Updated last week
- comseg☆19Updated last month
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆34Updated this week