SydneyBioX / BIDCell
Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
☆42Updated 9 months ago
Alternatives and similar repositories for BIDCell:
Users that are interested in BIDCell are comparing it to the libraries listed below
- Sub-cellular spatial transcriptomics Cell Segmentation☆64Updated last year
- comseg☆19Updated 3 months ago
- Integrated pipeline for multiplexed image analysis☆87Updated last month
- Spatial Single-Cell Analysis Toolkit☆90Updated 2 weeks ago
- ☆14Updated 3 years ago
- ☆32Updated last year
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆77Updated last year
- ☆35Updated last year
- Super-resolved spatial transcriptomics by deep data fusion☆73Updated 2 years ago
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆18Updated 2 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆35Updated 11 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆27Updated this week
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆30Updated 3 months ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆37Updated last year
- ☆35Updated this week
- Interoperability between SpatialData and the Xenium Explorer☆21Updated 9 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆54Updated 3 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆189Updated this week
- ☆28Updated 6 months ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆40Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆77Updated last month
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆54Updated last year
- Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA☆54Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆27Updated 7 months ago
- Python package for reading imaging mass cytometry (IMC) files☆15Updated last week
- A toolkit for processing multiplexed tissue images☆60Updated last month
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 11 months ago
- Segmentation error aware clustering for multiplexed imaging☆17Updated 3 months ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆45Updated 9 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆119Updated last week