CyLinter

CyLinter identifies and removes data associated with imaging artifacts in multiplex images for quality control in single-cell analysis of high-plex tissue profiles.

Key Features:

• Artifact Detection: Identifies noisy data points in multiplex images corrupted by artifacts such as folds, debris, antibody aggregates, optical aberrations, and image processing errors.
• Data Compatibility: Processes both pixel-level and single-cell data.
• Interactive Quality Control: Provides interactive functionality for identifying and removing artifact-associated data.
• Archival Specimen Support: Improves single-cell analysis especially for archival specimens sectioned many years before data collection, such as those from clinical trials.

Scientific Applications:

• Tumor Microenvironment Analysis: Enables quality control for single-cell analysis of complex cellular and acellular assemblies in tumors profiled with high-plex spatial profiling methods.
• Clinical Trial Specimen Analysis: Facilitates analysis of archival clinical trial specimens by removing artifact-corrupted data that would otherwise obscure meaningful biological interpretation.
• High-Plex Protein Profiling: Supports quality control for image-based profiling methods revealing intensities and spatial distributions of 20-100 proteins at subcellular resolution in 10^3-10^7 cells per specimen.

Methodology:

CyLinter applies interactive quality control to identify and remove data associated with imaging artifacts arising from imperfections in specimen preparation, data acquisition, image assembly, and feature extraction.