User Input

Brightness threshold* (facilitates nuclear detection in dim images)

Relative X/Y-Z resolution

Channel to segment

Nuclear diameter

Image noise level

MINS Output

Segmentation Z-stack with nuclei IDs

Nuclear volume

XYZ coordinates for each nucleus

Average and summation of fluorescence values for each fluorescence channel and nucleus

Advantages

Accurate segmentation (>85%) of nuclei throughout the stack — recognizes all occurrences of a nucleus in adjacent z-sections

Single cell resolution

Unsupervised segmentation of batches of embryos

Segmentation pipelines can either be saved and re-used or adjusted for each particular embryo