Table 1.

Summary of problems in cell-scaffold contact measurements and our approaches

Challenges	Approach
How to model cell, scaffold, and cell-scaffold contact from two-channel z-stacks?	Design statistical and geometrical models for segmentation
	Use the law of total probability in statistical models, and geometrical intersections in geometrical models for cell-scaffold contact detection
How to validate geometrical cell-scaffold contact models and assess the accuracy of all contact models?	Validate cylindrical and planar geometrical models using multi-view SEM and AFM measurements
	Assess the accuracy of all models applied to CLSM z-stacks by comparing single fiber radius measurements derived from CLSM z-stacks against the reference values extracted from SEM images
How to handle RAM and processing time requirements for TB-sized z-stack collection?	Reduce the amount of data to be processed by cropping ROIs defined by cell bounding boxes and reduce the processing time by utilizing parallel processing
How to verify quality of 3D contact measurements over several hundreds of [cell, scaffold] pairs of z-stacks?	Design a web system for visual verification using three orthogonal max 2D projections of cell and its segmentation, and six movies combining dynamic rotations of contacts and information layers of 3D cell-scaffold-contact per [cell, scaffold] pair