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PlexPipe - Multiplexed Image Analysis Pipeline

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Overview

PlexPipe is an multiplex analysis pipeline that processes images through a series of modular steps, transforming raw whole-slide TIFF images into quantitative single-cell data.

Key Features

  • Input Data: The pipeline accepts sets of individual TIFF files. It follows the naming conventions used by the Cell DIVE system. For specific requirements regarding file naming, refer to Input Data.
  • Remote Data Sourcing: Seamlessly source and transfer large-scale imaging datasets from institutional endpoints or personal collections using Globus. This ensures secure and reliable data movement directly into your processing environment (see: Globus Integration).
  • Data Integration: Outputs are stored as SpatialData objects, making them ready for downstream analysis within the scverse ecosystem or interactive exploration via the napari-spatialdata plugin.
  • Flexible Execution: PlexPipe can be implemented in two ways based on your needs:
    • Local/Interactive: Utilize the provided Python scripts or Jupyter Notebooks for smaller datasets or pipeline prototyping (see Execution Modes).
    • High-Throughput: For parallel processing and large-scale workflows, use the Nextflow-optimized version: plex-pipe-nextflow.