ciccalab / SIMPLILinks
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
☆37Updated last year
Alternatives and similar repositories for SIMPLI
Users that are interested in SIMPLI are comparing it to the libraries listed below
Sorting:
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆30Updated 4 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆10Updated 2 years ago
- Spatial Single-Cell Analysis Toolkit☆91Updated 2 weeks ago
- A toolkit for processing multiplexed tissue images☆62Updated this week
- Python package for reading imaging mass cytometry (IMC) files☆15Updated last week
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 11 months ago
- ☆32Updated last year
- ☆28Updated 7 months ago
- A pipeline to transform images into valuable analysis items☆13Updated this week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆35Updated last year
- ☆62Updated last week
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆14Updated 3 years ago
- A plugin to visualise 3D spatial single cell omics☆22Updated last year
- ☆27Updated 7 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆42Updated 10 months ago
- Interactive visualization of spatial omics data☆58Updated last week
- R package for visualization of highly multiplexed imaging data☆32Updated last week
- ☆35Updated last year
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆27Updated last week
- ☆29Updated last year
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆46Updated this week
- Histology Topography Cytometry Analysis Toolbox☆67Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆27Updated 8 months ago
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆18Updated 3 weeks ago
- Single-cell spatial proteomics analysis that makes you happy!☆28Updated this week
- comseg☆20Updated 3 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆80Updated last year
- Integrated pipeline for multiplexed image analysis☆90Updated 2 months ago
- Segmentation error aware clustering for multiplexed imaging☆18Updated 4 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆79Updated 2 months ago