simpleSeg

simpleSeg performs watershed-based segmentation of multiplexed cellular images in R based on the intensity of user-specified protein marker channels, enabling extraction of cell features such as marker expression and morphology, and provides normalization of single-cell data obtained from multiple images.

Key Features:

• Watershed-based segmentation: Segments cells in multiplexed cellular images using watershed algorithms based on user-specified protein marker channel intensities.
• Feature extraction: Enables extraction of cellular features including marker expression and morphology from segmented images.
• Single-cell data normalization: Normalizes single-cell data obtained from multiple images to account for batch or image-level variation.

Scientific Applications:

• Multiplexed imaging analysis: Identifies cell borders in multiplexed cellular images to enable downstream analysis of protein marker expression and cell morphology.
• Single-cell profiling: Extracts and stores single-cell features from images for further computational analysis.

Methodology:

simpleSeg implements watershed-based segmentation using intensity values from user-specified protein marker channels in multiplexed cellular images.