Ark-Analysis
A Python toolbox for analyzing multiplexed imaging data, featuring segmentation, pixel/cell clustering, and spatial analysis.
What is Ark-Analysis?
ark-analysis is a Python-based toolbox for analyzing multiplexed imaging data, providing an integrated pipeline for cell segmentation, pixel and cell clustering, and spatial analysis. It solves the problem of extracting quantitative, single-cell and spatial information from high-plex tissue images, such as those generated by MIBI or similar technologies. The pipeline guides users from raw image data to biological insights through a series of Jupyter notebooks.
Researchers and bioinformaticians working with multiplexed tissue imaging data, particularly in immunology, oncology, and spatial biology. It is suited for those needing to analyze high-plex images to identify cell phenotypes and their spatial relationships.
Developers choose ark-analysis for its complete, end-to-end workflow specifically designed for multiplexed imaging, its integration with state-of-the-art tools like Mesmer and Pixie, and its practical, notebook-based approach that combines automation with opportunities for manual refinement and visualization.
Overview
Integrated pipeline for multiplexed image analysis
Use Cases
Best For
- Analyzing MIBI or other multiplexed ion beam imaging data
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