The Stem Cell Colony App allows users to adjust tissue, cell, cluster, and gap detection parameters:

• Tissue detection: Select input image, define threshold value for tissue mask generation, adjust shrink radius, and remove tissue regions based on area (µm²).
• Membrane detection (cells): Configure Master/Membrane input images, remove small or intensity-out-of-range labels, adjust minimum variation sensitivity, kernel width/height, Gaussian filtering (Gauss Std), and area filtering.
• Cell seeds detection: Select input image, adjust threshold for seed extraction, define grow radius to reconstruct full cells, and remove seeds by area (µm²).
• Cluster gaps detection: Adjust grow radius for cluster gaps and remove gaps based on area thresholds.
• Clusters final detection: Select input image, define threshold for cluster segmentation, configure cluster ring exterior radius, and remove clusters by area (µm²).
• Manual correction: Add or delete Tissue, Cell Seeds, or Clusters using interactive drawing tools with adjustable thickness, fill, erase, apply, and cancel options.
• Overlay validation: Review Tissue, Cells, Clusters, and Cluster Gaps masks before exporting results.

The app provides quantitative measurements at colony, cluster, and gap levels:

• Total cluster area: Area (µm²) of detected clusters.
• Total cell area: Area (µm²) of detected cells within colonies.
• Cluster gaps: Total area (µm²) of gaps (cell-free regions) within clusters.
• Gap percentage: Cluster gaps area expressed as percentage of cluster area.
• Cluster classification: Classification of clusters based on number of cluster gaps and percentage of gap area per cluster.
• Statistics export: ROI/sample-based results generated via the Statistics Report tool.