MannLabs / scPortraitLinks
scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
☆102Updated this week
Alternatives and similar repositories for scPortrait
Users that are interested in scPortrait are comparing it to the libraries listed below
Sorting:
- Interactive visualization of spatial omics data☆73Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆84Updated 2 weeks ago
- Spatial Single-Cell Analysis Toolkit☆104Updated 5 months ago
- ☆80Updated last week
- Single-cell spatial proteomics analysis that makes you happy!☆45Updated last week
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated 3 weeks ago
- ☆62Updated last week
- comseg☆24Updated 10 months ago
- A pipeline to transform images into valuable analysis items☆16Updated 5 months ago
- Integrated pipeline for multiplexed image analysis☆100Updated 8 months ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆39Updated 2 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆40Updated last month
- Python package for Probe set selection for targeted spatial transcriptomics.☆47Updated 3 weeks ago
- ☆29Updated last year
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆80Updated 3 weeks ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Updated 5 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆66Updated this week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆38Updated last year
- ☆27Updated last year
- A toolkit for processing multiplexed tissue images☆67Updated this week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆91Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- A probabilistic cell typing algorithm for spatial transcriptomics.☆25Updated last month
- ☆39Updated last year
- Python API and Jupyter widget for Vitessce☆59Updated 3 weeks ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆61Updated last week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Updated last week
- Multiple-choice microscopy pipeline☆143Updated 2 weeks ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 5 months ago
- Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.☆18Updated 5 months ago