TheJacksonLaboratory / STQLinks
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
☆20Updated 3 months ago
Alternatives and similar repositories for STQ
Users that are interested in STQ are comparing it to the libraries listed below
Sorting:
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆58Updated 2 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆44Updated last year
- Histology Topography Cytometry Analysis Toolbox☆67Updated last year
- Spatial Single-Cell Analysis Toolkit☆94Updated last month
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆36Updated last year
- Python package for reading imaging mass cytometry (IMC) files☆15Updated last week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆82Updated last year
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆38Updated 2 years ago
- Integrated pipeline for multiplexed image analysis☆93Updated 4 months ago
- Multiple-choice microscopy pipeline☆136Updated last week
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆29Updated 2 months ago
- A pixel classification based multiplexed image segmentation pipeline☆99Updated last year
- Interactive visualization of spatial omics data☆64Updated last week
- QuPath extension to interactively align images☆24Updated last month
- ☆15Updated 3 years ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆28Updated 10 months ago
- Sub-cellular spatial transcriptomics Cell Segmentation☆66Updated last year
- ☆34Updated 3 weeks ago
- ☆38Updated last year
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆45Updated last month
- A toolkit for processing multiplexed tissue images☆62Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆80Updated last week
- ☆52Updated 4 years ago
- ☆65Updated last week
- A probabilistic cell typing algorithm for spatial transcriptomics.☆24Updated last month
- ☆36Updated this week
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated 6 months ago
- CODEX data processing code☆12Updated last month
- Interoperability between SpatialData and the Xenium Explorer☆24Updated last year
- comseg☆24Updated 6 months ago