BodenmillerGroup / ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
☆93Updated last year
Alternatives and similar repositories for ImcSegmentationPipeline:
Users that are interested in ImcSegmentationPipeline are comparing it to the libraries listed below
- Spatial Single-Cell Analysis Toolkit☆87Updated last week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆112Updated last week
- R package for visualization of highly multiplexed imaging data☆32Updated 9 months ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆57Updated 4 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆34Updated 10 months ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆45Updated 2 years ago
- Super-resolved spatial transcriptomics by deep data fusion☆72Updated 2 years ago
- Histology Topography Cytometry Analysis Toolbox☆67Updated last year
- Integrated pipeline for multiplexed image analysis☆85Updated this week
- A toolkit for processing multiplexed tissue images☆59Updated this week
- Image Mass Cytometry analysis pipeline☆25Updated 2 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆77Updated last year
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆10Updated 2 years ago
- ☆28Updated 5 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆41Updated 8 months ago
- Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA☆53Updated last year
- ☆50Updated 4 years ago
- ☆30Updated last month
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆37Updated last year
- Multiple-choice microscopy pipeline☆125Updated 3 weeks ago
- Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology☆112Updated 7 months ago
- ☆14Updated 3 years ago
- Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab☆94Updated 4 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆178Updated this week
- Join subcellular Visium HD bins into cells☆88Updated 3 months ago
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆51Updated last year
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 9 months ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆170Updated 3 months ago
- Code for the spatialLIBD R/Bioconductor package and shiny app☆91Updated last week
- Spatial mapping of cell types by integration of transcriptomics data☆90Updated 2 years ago