hubmapconsortium / codex-pipelineLinks
CODEX data processing code
☆12Updated 4 months ago
Alternatives and similar repositories for codex-pipeline
Users that are interested in codex-pipeline 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…☆65Updated 6 months ago
- Integrated pipeline for multiplexed image analysis☆99Updated 7 months ago
- A pipeline to transform images into valuable analysis items☆15Updated 5 months ago
- Multiple-choice microscopy pipeline☆138Updated last week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆38Updated last year
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆21Updated 6 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆46Updated last year
- A toolkit for processing multiplexed tissue images☆65Updated last week
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆62Updated last year
- Histology Topography Cytometry Analysis Toolbox☆69Updated 3 weeks ago
- Spatial Single-Cell Analysis Toolkit☆103Updated 4 months ago
- A pixel classification based multiplexed image segmentation pipeline☆101Updated last year
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated last week
- An introduction to deepcell and deep learning☆154Updated last year
- Piecewise alignment for layers of mosaics☆29Updated 2 months ago
- Sub-cellular spatial transcriptomics Cell Segmentation☆68Updated 2 years ago
- Accessible and interoperable whole slide image analysis☆157Updated this week
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆100Updated last week
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆39Updated last month
- Interactive visualization of spatial omics data☆72Updated last week
- ☆35Updated last year
- QuPath extension to run StarDist nucleus detection☆47Updated 4 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆11Updated 2 years ago
- comseg☆24Updated 9 months ago
- Super-resolved spatial transcriptomics by deep data fusion☆74Updated 2 years ago
- QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis☆32Updated 4 months ago
- multimodal whole slide image registration in a graph structure☆95Updated last year
- ☆24Updated 2 years ago
- ☆56Updated 9 months ago
- ☆18Updated last year