EliHei2 / segger_devLinks
a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
☆81Updated last week
Alternatives and similar repositories for segger_dev
Users that are interested in segger_dev are comparing it to the libraries listed below
Sorting:
- Spatial Single-Cell Analysis Toolkit☆105Updated 5 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆48Updated last week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆38Updated last year
- ☆83Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆84Updated last month
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆251Updated this week
- Python package for Probe set selection for targeted spatial transcriptomics.☆47Updated last month
- Join subcellular Visium HD bins into cells☆130Updated last month
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆93Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆145Updated last week
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- Code used to benchmark Xenium☆72Updated last year
- ☆55Updated last week
- Interoperability between SpatialData and the Xenium Explorer☆25Updated last year
- Interactive visualization of spatial omics data☆73Updated last week
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Updated 6 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆144Updated last week
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆104Updated this week
- comseg☆24Updated 10 months ago
- ☆62Updated last week
- A pipeline to transform images into valuable analysis items☆16Updated 6 months ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆88Updated last week
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆46Updated last year
- A probabilistic cell typing algorithm for spatial transcriptomics.☆25Updated last month
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆70Updated last month
- A toolkit for processing multiplexed tissue images☆67Updated this week
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆22Updated 8 months ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 5 months ago
- ☆42Updated last month
- Integrated pipeline for multiplexed image analysis☆100Updated this week