ciccalab / SIMPLILinks
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
β38Updated 2 years ago
Alternatives and similar repositories for SIMPLI
Users that are interested in SIMPLI are comparing it to the libraries listed below
Sorting:
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics π₯π¬β¨β53Updated 2 weeks ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"β10Updated 2 years ago
- A toolkit for processing multiplexed tissue imagesβ61Updated 3 weeks ago
- An Interactive Image Segmentation Filter for Multiplex Microscopyβ30Updated 5 months ago
- Histology Topography Cytometry Analysis Toolboxβ67Updated last year
- R package for visualization of highly multiplexed imaging dataβ32Updated last month
- Integrated pipeline for multiplexed image analysisβ91Updated 3 months ago
- β27Updated 9 months ago
- Spatial Single-Cell Analysis Toolkitβ92Updated 2 weeks ago
- β63Updated 2 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics dataβ80Updated 3 weeks ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.β27Updated 9 months ago
- β27Updated 9 months ago
- β54Updated last week
- β29Updated last year
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cβ¦β14Updated 3 years ago
- β36Updated last year
- Python package for reading imaging mass cytometry (IMC) filesβ15Updated last week
- ClusterMap for multi-scale clustering analysis of spatial gene expressionβ45Updated last month
- A pixel classification based multiplexed image segmentation pipelineβ96Updated last year
- β12Updated 2 months ago
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.β28Updated last month
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mappingβ81Updated last year
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy imagesβ47Updated this week
- MERFISH decoding softwareβ26Updated 2 years ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics dataβ43Updated 11 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaβ¦β58Updated last month
- A probabilistic cell typing algorithm for spatial transcriptomics.β24Updated 3 weeks ago
- Multiple-choice microscopy pipelineβ133Updated 4 months ago
- A plugin to visualise 3D spatial single cell omicsβ22Updated 3 weeks ago