SurfCut

SurfCut extracts two-dimensional cell contours from three-dimensional confocal image stacks to enable quantitative analysis of cell shape in relatively flat biological tissues.

Key Features:

• ImageJ macro: Implemented as a macro for ImageJ to integrate with ImageJ-based image-processing workflows.
• 2D extraction from 3D stacks: Segments cells in two dimensions from three-dimensional confocal image stacks to produce cell contours.
• High-throughput processing: Optimized for batch processing to handle large datasets.
• Automation: Supports automation for consistent, repeatable extraction of contours.
• Optimized for flat samples: Designed for relatively flat samples with shallow curvature.
• Interoperability with PaCeQuant: Produces contours that can be assessed using PaCeQuant for downstream morphometric analysis.

Scientific Applications:

• Epithelial cell morphology (Drosophila embryogenesis): Quantifies epithelial cell shape during Drosophila embryogenesis by extracting 2D contours from confocal stacks.
• Plant epidermis pavement cell analysis (cotyledon epidermis): Enables quantitative shape and area measurements of plant epidermis pavement cells such as cotyledon epidermis.
• Quantitative analysis of flat tissues: Facilitates morphological measurements and area quantification in relatively flat biological samples.

Methodology:

Implemented as an ImageJ macro that segments cells in 2D from 3D confocal stacks, optimized for relatively flat samples with shallow curvature; results have been compared to MorphoGraphX (MGX) and assessed using PaCeQuant.