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Analysis of Multidimensional Microscopy Data Using Cell-ACDC
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Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging.

Eric Czech1, Bulent Arman Aksoy2, Pinar Aksoy2

  • 1Microbiology and Immunology Department at Medical University of South Carolina, Charleston, USA. eric@hammerlab.org.

BMC Bioinformatics
|September 4, 2019
PubMed
Summary
This summary is machine-generated.

Cytokit is an open-source software tool that processes large multiplexed immunofluorescence datasets, enabling detailed cell analysis for disease research. It provides GPU-accelerated pipelines and interactive tools for high-throughput biological data quantification.

Keywords:
Automatic image processingCellProfilerData explorationData visualizationGPUMultiplexed fluorescence imaging

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Microscopy Image Analysis

Background:

  • Multiplexed in-situ fluorescent imaging preserves spatial, morphological, and marker data crucial for understanding disease.
  • Advancements in imaging protocols necessitate robust software for processing large, complex datasets.
  • Spatial information is key to unlocking new diagnostic and disease progression insights.

Purpose of the Study:

  • To provide and validate software for processing large data from multiplexed in-situ fluorescent imaging.
  • To develop an end-to-end image processing pipeline for high-dimensional microscopy data.
  • To enable efficient analysis of spatial, graphical, expression, and morphological cell properties.

Main Methods:

  • Developed a GPU-accelerated, end-to-end image processing pipeline.
  • Implemented efficient I/O strategies for high-dimensional microscopy data.
  • Integrated an interactive user interface for cross-filtering cell properties.
  • Adapted and sourced image processing operations from existing deep learning models and open-source packages.

Main Results:

  • Cytokit efficiently processes large (100+ GB) multiplexed immunofluorescence datasets.
  • Demonstrated efficacy by comparing results with independent assays.
  • Validated reproducibility of previously published results using public datasets.
  • Supports batch-oriented, high-throughput analysis for technical users.

Conclusions:

  • Cytokit is an open-source collection of tools for quantifying and analyzing individual cells in large fluorescent microscopy datasets.
  • Facilitates high-throughput analysis of multiplexed antibody labeling data.
  • Source code, documentation, and data are publicly available under Apache License 2.0.