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 |