Publication Date

Spring 5-5-2024

Document Type


First Advisor

Yasui, Linda

Degree Name

B.S. (Bachelor of Science)


Department of Biological Sciences


Neuroinflammation is an inflammatory response in the brain that can be caused by different stressors such as diseases and/or external factors such as traumatic brain injuries. It is important to note duration and intensity of neuroinflammation levels when determining the impacts of these stressors to the brain environment. During neuroinflammation, a type of immune cell that becomes activated in the brain is called microglial cells. Microglial cells play a role in progression of the pathophysiological effects from the brain stressor. Studying changes in microglial cell shape provides evidence of the degree of neuroinflammation in the brain. Researchers can quantify neuroinflammation based on the visualization of microglial shape changes from highly branched, or ramified, shapes (inactivated microglial cells) to more spherical microglial cell shapes (activated microglial cells). The degree of microglial cell activation elucidates the degree of neuroinflammation in different brain regions after exposure to brain stressors. The goal of this study is to develop an image analysis workflow for microglial cell activation found in 40 µm rodent brain cryosections that were stained using the antibody to microglial cells, iba1, and a secondary antibody linked to Alexafluor 568 to stain microglial cells red. A Zeiss LSM 900 with Airyscan 2 confocal laser scanning microscope was used to acquire image data, and Imaris 9.1.1 was used to perform 3D rendering and microglial cell segmentation to identify and quantify microglial activation. The workflow developed will be used to determine the degree of neuroinflammation from stress in rodent model systems.