SchapiroLabor / histoCATLinks
Histology Topography Cytometry Analysis Toolbox
☆67Updated 2 years ago
Alternatives and similar repositories for histoCAT
Users that are interested in histoCAT are comparing it to the libraries listed below
Sorting:
- A pixel classification based multiplexed image segmentation pipeline☆100Updated last year
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆15Updated 3 years ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆48Updated 3 years ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆64Updated 9 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆36Updated last year
- Spatial Single-Cell Analysis Toolkit☆94Updated last month
- Image Mass Cytometry analysis pipeline☆26Updated 2 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆11Updated 2 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆38Updated 2 years ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆86Updated last year
- Integrated pipeline for multiplexed image analysis☆93Updated 4 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆59Updated 3 months ago
- R package for visualization of highly multiplexed imaging data☆33Updated 2 months ago
- ☆38Updated last year
- Python package for reading imaging mass cytometry (IMC) files☆15Updated last week
- Multiple-choice microscopy pipeline☆136Updated last week
- ☆29Updated last year
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆54Updated 2 months ago
- A toolkit for processing multiplexed tissue images☆62Updated 2 weeks ago
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆20Updated 3 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆29Updated 11 months ago
- ☆27Updated 10 months ago
- Subpopulation detection in high-dimensional single-cell data☆70Updated 4 years ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆44Updated last year
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆82Updated 3 weeks ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆64Updated last month
- ☆34Updated last month
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated 2 weeks ago
- R based workflow for multiplexed imaging data☆32Updated last month
- QuPath extension to run StarDist nucleus detection☆43Updated last month