ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
β35Updated last year
Alternatives and similar repositories for SIMPLI:
Users that are interested in SIMPLI are comparing it to the libraries listed below
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics π₯π¬β¨β52Updated 9 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"β10Updated 2 years ago
- Spatial Single-Cell Analysis Toolkitβ86Updated last month
- An Interactive Image Segmentation Filter for Multiplex Microscopyβ28Updated last month
- β25Updated 5 months ago
- β30Updated last year
- R package for visualization of highly multiplexed imaging dataβ32Updated 8 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics dataβ40Updated 8 months ago
- β27Updated 5 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information β¦β33Updated 10 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy imagesβ42Updated this week
- Interactive visualization of spatial omics dataβ51Updated last week
- 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
- Histology Topography Cytometry Analysis Toolboxβ67Updated last year
- β34Updated 11 months ago
- A toolkit for processing multiplexed tissue imagesβ58Updated 2 weeks ago
- Python package for reading imaging mass cytometry (IMC) filesβ13Updated this week
- https://sparrow-pipeline.readthedocs.io/en/latest/β26Updated 2 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics dataβ76Updated 3 weeks ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.β26Updated 5 months ago
- β28Updated last month
- β46Updated last week
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive fβ¦β56Updated 4 months ago
- β51Updated 2 weeks ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mappingβ75Updated last year
- β14Updated 3 years ago
- Integrated pipeline for multiplexed image analysisβ84Updated this week
- QuPath extension to interactively align imagesβ22Updated 3 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaβ¦β51Updated last month
- Single-cell spatial proteomics analysis that makes you happy!β23Updated last week