Segmentation

Multiple segmentation workflows exist, each focused on different aspects of different organisms. Please see the different workflow sections below.

Zebrafish Segmentation

MCAM Zebrafish segmentation is based on a 2D-UNet which has become a mainstay in biomedical image analysis. Multiple zebrafish segmentation models are actively in use including brightfield and fluorescence modalities. Once segmentation masks have been inferred for each fish, further analysis can be performed within these regions such as area measurement, blob counting (to quantify cell counts for example), and bulk fluorescence intensity quantification.