ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
ā37Updated last year
Alternatives and similar repositories for SIMPLI:
Users that are interested in SIMPLI are comparing it to the libraries listed below
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"ā10Updated 2 years ago
- An Interactive Image Segmentation Filter for Multiplex Microscopyā30Updated 2 months ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics š„š¬āØā52Updated 10 months ago
- Spatial Single-Cell Analysis Toolkitā91Updated 3 weeks ago
- Python package for reading imaging mass cytometry (IMC) filesā14Updated last week
- ā28Updated 6 months ago
- ā32Updated last year
- R package for visualization of highly multiplexed imaging dataā32Updated 9 months ago
- A plugin to visualise 3D spatial single cell omicsā22Updated last year
- ā26Updated 6 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics dataā43Updated 9 months ago
- ā34Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.ā27Updated 7 months ago
- A toolkit for processing multiplexed tissue imagesā60Updated 3 weeks ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information ā¦ā35Updated 11 months ago
- ā14Updated 3 years ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cā¦ā14Updated 3 years ago
- ā30Updated 11 months ago
- Histology Topography Cytometry Analysis Toolboxā67Updated last year
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.ā27Updated 2 months ago
- Segmentation error aware clustering for multiplexed imagingā17Updated 3 months ago
- Single-cell spatial proteomics analysis that makes you happy!ā25Updated this week
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide imagesā18Updated 2 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics dataā77Updated 3 weeks ago
- Image Mass Cytometry analysis pipelineā25Updated 2 months ago
- comsegā19Updated 2 months ago
- Interoperability between SpatialData and the Xenium Explorerā21Updated 8 months ago
- ā57Updated this week
- Interactive visualization of spatial omics dataā52Updated this week
- Integrated pipeline for multiplexed image analysisā86Updated 3 weeks ago