Seeing Cells Clearly: Evaluating Machine Vision Strategies for Microglia Centroid Detection in 3D Images

TL;DR

This study compares three machine vision tools—ilastik, 3D Morph, and Omnipose—for detecting microglia cell centers in 3D brain images, highlighting differences in their detection capabilities and implications for brain health analysis.

Contribution

It provides a comparative evaluation of three existing tools for microglia centroid detection in 3D microscopy images, revealing their varying detection performance.

Findings

Different tools detect microglia centers differently.

Detection results influence interpretation of brain health.

Each tool has unique strengths and limitations.

Abstract

Microglia are important cells in the brain, and their shape can tell us a lot about brain health. In this project, I test three different tools for finding the center points of microglia in 3D microscope images. The tools include ilastik, 3D Morph, and Omnipose. I look at how well each one finds the cells and how their results compare. My findings show that each tool sees the cells in its own way, and this can affect the kind of information we get from the images.