SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
☆39Sep 23, 2025Updated 8 months ago
Alternatives and similar repositories for SIMPLI
Users that are interested in SIMPLI are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Spatial RNA velocity☆10Oct 3, 2024Updated last year
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆12Mar 3, 2023Updated 3 years ago
- RAnking Markers for CEll Segmentation☆12Feb 22, 2022Updated 4 years ago
- R package for visualization of highly multiplexed imaging data☆36May 27, 2025Updated 11 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆71Dec 2, 2025Updated 5 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Napari Visualization tool for Trackmate > 6.0 XML files for 2/3D + time tracks. Available via pip package napatrackmater.☆18Oct 8, 2025Updated 7 months ago
- Spatial direct messaging detected by bivariate Moran☆32Jul 16, 2025Updated 10 months ago
- Kaibu -- a progressive web app for visualizing and annotating multi-dimensional images.☆35Apr 4, 2025Updated last year
- Toolkit to help develop and run QuPath scripts from Eclipse and other IDEs, including over remote connections. (See README.md for more in…☆17Aug 19, 2020Updated 5 years ago
- ngio is a Python library to streamline OME-Zarr image analysis workflows.☆49May 18, 2026Updated last week
- ☆28Nov 21, 2019Updated 6 years ago
- Next generation of SuRVoS☆10Oct 11, 2023Updated 2 years ago
- A toolkit for processing multiplexed tissue images☆70Updated this week
- Explainable AI model of cell behavior☆20Apr 4, 2023Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022☆10Jan 12, 2022Updated 4 years ago
- A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, i…☆31Mar 14, 2025Updated last year
- Robust quad-tree based registration on whole slide images☆20Apr 2, 2025Updated last year
- ☆29Sep 4, 2023Updated 2 years ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆48Aug 7, 2021Updated 4 years ago
- ☆20May 1, 2025Updated last year
- dask empowered fast4dreg☆16Mar 11, 2026Updated 2 months ago
- Histology Topography Cytometry Analysis Toolbox☆69Mar 23, 2026Updated 2 months ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆17Sep 26, 2021Updated 4 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Codes to regenerate figures for mutagen paper☆12Apr 8, 2021Updated 5 years ago
- An R package for extracting mutational signatures from vcf files☆11Feb 13, 2025Updated last year
- Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz☆11Apr 22, 2020Updated 6 years ago
- Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile☆21Sep 8, 2023Updated 2 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆96Apr 30, 2026Updated 3 weeks ago
- A module with convenience functions for writing Python code that interacts with OMERO.☆47Dec 4, 2025Updated 5 months ago
- Automatically annotate cell types, consistently across samples.☆21May 14, 2026Updated last week
- MultiModal Big Image Data Sharing and Exploration☆20Jan 13, 2023Updated 3 years ago
- shrimPy: Smart High-throughput Robust Imaging & Measurement in Python☆13May 11, 2026Updated last week
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Unsupervised cell functional annotation for single-cell RNA-Seq☆22Jan 11, 2023Updated 3 years ago
- CloudReg☆11Apr 5, 2024Updated 2 years ago
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆32Apr 9, 2026Updated last month
- Python libraries for loading, running and packaging bioimage.io models☆38Updated this week
- Course website for Genomic Data Visualization 2022☆16Dec 28, 2022Updated 3 years ago
- Fast4DReg is a Fiji script for quick drift correction in time-lapse 3D-stacks. The script can be used to correct drift in all x-, y- and/…☆41Apr 21, 2025Updated last year
- A collection of materials used in Undergraduate Bioinformatics Club (UBIC) workshops at UCSD.☆50Feb 19, 2026Updated 3 months ago