nf-core / mcmicroLinks
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
☆25Updated this week
Alternatives and similar repositories for mcmicro
Users that are interested in mcmicro are comparing it to the libraries listed below
Sorting:
- ☆23Updated 2 weeks ago
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)☆13Updated last week
- Image Mass Cytometry analysis pipeline☆26Updated 5 months ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 4 months ago
- Tools to handle IMC data☆23Updated 3 years ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆16Updated 4 years ago
- ☆30Updated last year
- An R package for performing cell typing in SMI and other single cell data☆43Updated 6 months ago
- ☆29Updated last year
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆16Updated 2 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆139Updated last week
- Identification of spatial homogeneous regions☆21Updated last month
- Python package for Probe set selection for targeted spatial transcriptomics.☆45Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆38Updated 2 weeks ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Updated last week
- Single-cell spatial proteomics analysis that makes you happy!☆43Updated this week
- R package for visualization of highly multiplexed imaging data☆34Updated 5 months ago
- Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)☆30Updated this week
- Segmentation error aware clustering for multiplexed imaging☆19Updated 10 months ago
- ☆62Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆84Updated this week
- Interoperability between SpatialData and the Xenium Explorer☆25Updated last year
- List of Spatial Transcriptomics related Tools organized per category☆83Updated last week
- Analyzing cellular niches in spatial transcriptomics data☆32Updated last year
- ☆45Updated this week
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆57Updated 4 months ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆50Updated 3 years ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆62Updated 3 months ago
- ☆77Updated last week
- Multi-modal single cell analysis pipelines☆59Updated 3 weeks ago