Bioimage analysis automation

Flowchart describes principal input-to-output image analysis workflow.

My favorite image analysis tools

Image preprocessing

Median filter to subtracts "salt and pepper" noise and refines vesicle detection (red spots) in human vascular smooth muscle cells.

Image segmentation

Segmentation algorithm detects human vascular smooth muscle cell nucleus stained with fluorescent dye (right) and marks them with yellow perimeter mask (left).

Feature extraction

Nuclear classification algorithm. A workflow detects human vascular smooth muscle cell nucleus stained with fluorescent dye, analyses a secondary fluorescent label within masked nuclear perimeter, and using machine learning algorithm k-means method determines intensity classes that are circled in different colors.