huangch / qust
QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis
☆10Updated last week
Related projects ⓘ
Alternatives and complementary repositories for qust
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆30Updated 6 months ago
- Multiple-choice microscopy pipeline☆113Updated last month
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆35Updated 4 months ago
- Integrated pipeline for multiplexed image analysis☆76Updated 2 weeks ago
- QuPath extension to interactively align images☆20Updated 3 months ago
- ☆29Updated 11 months ago
- The official QuPath extension for InstanSeg☆10Updated last week
- QuPath extension to run StarDist nucleus detection☆35Updated 2 months ago
- ☆33Updated 7 months ago
- ☆25Updated 6 months ago
- Python package for reading imaging mass cytometry (IMC) files☆12Updated this week
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆35Updated last year
- an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.☆65Updated 2 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆143Updated this week
- Histology Topography Cytometry Analysis Toolbox☆66Updated last year
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆45Updated 3 weeks ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆12Updated 3 years ago
- Trained only with subject-level labels, NaroNet discovers phenotypes, neighborhoods, and areas with the highest influence when classifyin…☆15Updated 10 months ago
- Spatial Single-Cell Analysis Toolkit☆74Updated this week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆69Updated 11 months ago
- Sub-cellular spatial transcriptomics Cell Segmentation☆56Updated last year
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆42Updated 2 years ago
- ☆14Updated 2 years ago
- Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration☆41Updated this week
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆48Updated 8 months ago
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆25Updated 3 weeks ago
- ☆31Updated last month
- Piecewise alignment for layers of mosaics☆20Updated 2 weeks ago
- CellSNAP: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆14Updated last month