Daniela Kaufer, Professor

Closed (1) Developing an automated image analysis pipeline for quantifying oligodendrocytes and myelination in rodent brains

Applications for fall 2021 are now closed for this project.

Myelin is the insulated multilayer membrane, which plays an essential role in the functional properties of neurons. In the central nervous system (CNS), oligodendrocytes generate myelin in the axonal and dendritic processes of neurons. Throughout the lifetime, the degree of myelination can be changed by learning or functional experience via oligodendrogenesis. Maladaptive myelination in this process may lead to various neurological disorders by altering temporal activities and synchronization of distinct neural circuits.

Previous literature has demonstrated the key relationships between myelination, oligodendrogenesis and various neuropsychiatric disorders. In Dr. Kaufer's lab, we are particularly interested in understanding the detailed mechanisms of how myelination and oligodendrocytes are regulated upon exposure to traumatic stress in rodent brains using various imaging toolkits including immunofluorescence and fluorescent/confocal microscope imaging.

The conventional analysis of fluorescent imaging would include manual counting of individual oligodendrocyte cells that are co-localized with proliferating markers in given brain regions using a Java-based image quantification program (ImageJ or FIJI). However, this method takes prolonged time solely for quantification and resulting delays in imaging data analysis. Thus, the goal of the project is to develop an automated imaging analysis pipeline and perform a series of analyses to identify the proliferating oligodendrocyte cells and myelination.


The student researcher will be involved in developing a pipeline by creating a macro script for ImageJ, by integrating Python scripts to an image analysis software (CellProfiler) and performing a series of image analyses using the above tools and a rodent brain atlas. The student researcher is also expected to be actively involved in journal club, lab meetings, and individual meetings with their direct supervisor along with minor lab duties. Upon completion of the project, the student researcher will learn the imaging and statistical analysis process in a biomedical research setting and basic neuroanatomy of the rodent brain.

Day-to-day supervisor for this project: MeeJung Ko, Post-Doc

Qualifications: Applicants must be self-motivated to learn, demonstrate a strong work and research ethic, and be able to work both independently and as a team. Given the nature of the project, computational skills (e.g. Python or MATLAB) are highly recommended. Previous records of general biology and physics would be preferred. Also, previous experiences with a microscope and/or imaging analysis are a plus.

Weekly Hours: 9-11 hrs

Related website: https://www.kauferlab.com