SIMPLI

SIMPLI performs spatially resolved identification and quantification of cells and marker expression from multiplexed histological imaging data to enable tissue phenotyping at single-cell resolution.

Key Features:

• Technology-Agnostic Pipeline: Processes multiplexed imaging data from different platforms using a unified, technology-agnostic pipeline.
• Spatially Resolved Single-Cell Analysis: Performs spatially resolved single-cell phenotyping while preserving spatial context within tissue sections.
• Customizable Workflow: Supports customizable workflows across computational environments and enables workflow parallelization for large datasets.
• Comprehensive Output Generation: Generates tabular and graphical outputs at each analytical step.
• Cell-Independent Quantifications: Performs cell-independent quantifications of marker expression to characterize tissue features not captured at the cellular level.
• Containerized Implementation: Provides a containerized implementation to ensure reproducibility and portability across computational environments.

Scientific Applications:

• Histopathology: Enables spatially resolved tissue phenotyping and marker quantification for histopathological analysis.
• Developmental Biology: Supports analysis of spatial organization and phenotypic changes during development.
• Immunology: Facilitates characterization of immune cell phenotypes and their spatial relationships within tissues.
• Translational Research: Enables spatial phenotyping applicable to translational studies.

Methodology:

The pipeline performs raw image processing followed by spatially resolved single-cell analysis and cell-independent quantifications, with support for parallelized workflows and containerized execution.