Light Microscopy Core Research Associate
Case Western Reserve University: SCHOOL OF MEDICINE: School of Medicine – Main Campus

Location: 6th Floor Robbins
Open Date: Oct 12, 2023


The position's goal is to assist the Light Microscopy Core in helping our collaborators use our spatial transcriptomic system and other advanced microscopy instruments (e.g., light-sheet microscopy, confocal microscopy, etc.). The research associate will report directly to the core manager. Primary goals will be helping with the preparation of slides for our spatial multi-omic imaging system and analysis of the subsequent data. Other goals can include providing in-depth training, assisting with tissue preparation for light-sheet microscopy, aiding with user troubleshooting, maintaining instruments, advising on image analysis, etc.


1.Plan and execute experiments for research projects designed by the principal investigator and may design experiments independently and in collaboration with the PI. Assist with and coordinate experiments performed by other lab members, ensuring adequate resources, assisting with experimental design and analysis. Coordinate with collaborators to prepare slides for spatial-omic imaging. This includes consulting with the histology core to get either formalin-fixed paraffin-embedded (FFPE) or fresh frozen (FE) tissue slides and preparing the slides over a two-day period for spatial multi-omic imaging. (25%)

2. Mentor, assist, and train lab staff, graduate students, and our collaborators to oversee and analyze their spatial multi-omic data. This includes using programs like Seurat, SquidPy, scVerse, scVI, etc. This will involve teaching other members of the lab techniques and scientific discovery methods, including students and post-docs. Assist and teach both established and new research techniques to other lab members to facilitate their experiments. Coordinate trainings for lab members with the EHS and others, as needed (35%)

3.Maintain a cutting-edge analysis pipeline for our spatial multi-omic imaging. This includes staying up on the most current techniques used in the research community. Assist the PI in and independently develop new techniques and protocols. Train lab members on new techniques. Assess, update, and develop new standard operating procedures (SOPs) for the lab. Assist lab staff and collaborators with all aspects of processing and handling essential and big data (15%)

4. Assist and train collaborators to analyze their imaging data. This includes using programs like Cellpose, Imaris, ImageJ, etc May supervise research assistants and technicians. Supervise the research and technical work performed by other lab members, ensuring proper lab procedures are followed, and their safety, and ensuring adequate resources are provided. Assist and train collaborators to prepare their tissues for light-sheet microscopy (e.g., optical clearing, whole-mount staining, etc.) (15%)


1. Perform other duties as assigned (5%)

2. Assist with maintenance or training on other instruments (3%)

3. Hold training sessions or tours for educational purposes (2%)


Department: Frequent contact with Core Faculty Director, Core Manager, and other staff.

University: Frequent contact with principal investigators and other research personnel and faculty and staff within the School of Medicine to collaborate on complex research. Regular contact with administrative offices and research administration within the school and the university to resolve issues.

External: Frequent contact with collaborating institutions and agencies who have similar instrumentation and analysis pipelines to understand best practices or wish to collaborate with us.

Students: Daily contact with student employees to maintain workflow, make adjustment to work, and/or establish procedures.


The position will include limited supervisory responsibility. The applicant may be asked to help supervise and train staff and users of our equipment.

About Case Western Reserve University

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