Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)
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Oct 8, 2026 - Python
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multiplexed-imaging
Here are 27 public repositories matching this topic...
Integrated pipeline for multiplexed image analysis
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Sep 18, 2026 - Jupyter Notebook
Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
browser viewer spatial spatial-analysis spatial-data omics spatial-proteomics mcd histology spatial-transcriptomics zarr visium multiplexed-imaging imaging-mass-cytometry spatial-omics xenium spatial-biology
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Oct 12, 2026 - Python
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
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Mar 14, 2024 - Jupyter Notebook
astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
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Sep 2, 2026 - Python
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
workflow pipeline nextflow image-processing spatial stitching registration segmentation image-analysis single-cell microscopy ome-tiff nf-core tma bioformats multiplexed-imaging
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Oct 8, 2026 - Nextflow
Probabilistic topic model for identifying cellular micro-environments.
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Jul 6, 2023 - Python
Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io) [NeurIPS'26]
python spatial-analysis spatial-data image-analysis spatial-proteomics biomarker-discovery deeplearning-ai single-cell-analysis spatial-transcriptomics tumor-microenvironment clinical-workflow multiplexed-imaging histology-images
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Sep 25, 2026 - Python
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
image-processing proteomics phenotyping multichannel single-cell spatial-data-analysis ome-tiff cell-segmentation whole-slide-imaging proteomics-data-analysis digital-slide-archive cell-cell-interaction multiplexed-imaging multiplexed-imaging-analysis mibiscope spatial-biology
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Feb 29, 2024 - JavaScript
A Python package for unsupervised analysis of spatial (prote)omics data.
image-analysis spatial-proteomics spatial-statistics pathology multiplexed-imaging scverse pathoplex
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Jul 23, 2026 - Python
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
spatial-analysis spatial-proteomics spatial-data-analysis mass-cytometry denoising-images multiplexed-imaging multiplexed-imaging-analysis
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Aug 5, 2025 - Jupyter Notebook
spora [bench] is a benchmark for spatial proteomics foundation models.
spatial-proteomics digital-pathology pathology precision-oncology multiplexed-imaging foundation-models
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Oct 9, 2026 - Python
MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds
image-processing image-registration manifold-learning multiplexed-imaging manifold-alignment cobordism cobordism-learning
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Nov 25, 2021 - Jupyter Notebook
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
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Dec 3, 2024 - Jupyter Notebook
A workflow designed to perform multiplexed image analysis, specialising in (but not limited to) analysis of metal distribution in LA-ICP-TOFMS data.
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Sep 6, 2026 - Jupyter Notebook
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
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Dec 3, 2024 - Jupyter Notebook
Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.
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Feb 21, 2023 - Rust
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Sep 23, 2026 - Jupyter Notebook
Analysis pipelines for paper Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures
machine-learning computer-vision deep-learning image-processing spatial-analysis image-analysis single-cell microscopy spatial-proteomics cell-segmentation 3d-segmentation bioimage-analysis spatial-transcriptomics fluorescence-microscopy multiplexed-imaging microscopy-image-analysis
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Sep 29, 2026 - Jupyter Notebook
Perform RESTORE normalization on multiplexed imaging data.
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Jun 22, 2023 - Python
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