angelolab / pixieLinks
Pixie pipeline described in Liu et al., Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
☆12Updated 2 years ago
Alternatives and similar repositories for pixie
Users that are interested in pixie are comparing it to the libraries listed below
Sorting:
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆34Updated 6 months ago
- Interoperability between SpatialData and the Xenium Explorer☆25Updated last year
- ☆30Updated last year
- ☆41Updated last week
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆23Updated 9 months ago
- A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from …☆25Updated this week
- Single-cell spatial proteomics analysis that makes you happy!☆51Updated this week
- ☆88Updated this week
- Segmentation error aware clustering for multiplexed imaging☆19Updated last year
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆116Updated 2 weeks ago
- ☆65Updated this week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Updated last week
- Sub-cellular spatial transcriptomics Cell Segmentation☆68Updated 2 years ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆45Updated 7 months ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆25Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Updated 2 months ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆56Updated 7 months ago
- ☆35Updated last week
- CAST package☆42Updated last year
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated 2 months ago
- comseg☆24Updated 11 months ago
- Spatial Single-Cell Analysis Toolkit☆108Updated 3 weeks ago
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆41Updated 11 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆105Updated last week
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆15Updated last year
- MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics☆16Updated last month
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆39Updated last month
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆46Updated last year
- Test genes for Spatial Variation☆15Updated last year
- Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…☆42Updated last year