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Postdoctoral Research Fellowship in Optical Neuroimaging

Wang Lab, University of Michigan, Ann Arbor, MI, United States

Employer Description:

PI: TD Wang, MD,PhD, University of Michigan

Description. The Wang Lab at the University of Michigan is seeking a highly motivated Postdoctoral Research Fellow for an NIH-funded program in optical imaging, miniature microscopy, and quantitative analysis of large-scale brain-imaging datasets. The fellow will help achieve high-resolution, real-time imaging of neural activity in freely behaving mice and will develop computational methods that make longitudinal multiphoton volumes scientifically usable. The role sits at the intersection of instrumented in vivo imaging and computer vision. Advance longitudinal brain imaging with a custom, fiber-coupled, head-mounted miniature confocal microscope (3-axis scanner, multiplexed fluorescence detection, subcellular resolution, large field of view, random-access scanning). The other part processes multiphoton and related 3D fluorescence datasets: registering sequential volumes, quantifying rigid and non-rigid displacement, correcting tissue and animal motion, establishing objective registration metrics, and tracking labeled structures over time. The appointment supports the NIH P41 Imaging Center. The fellow will work with Center investigators in neuroscience, engineering, and pathology, and will analyze both Wang Lab recordings and collaborating-lab datasets — including repeated multiphoton imaging of the same brain region over days to weeks. We welcome applicants strongest on the experimental side, strongest on the computational side, or fluent in both.

In vivo optical neuroimaging

•  Perform in vivo imaging with a custom-built miniature confocal microscope to monitor neural structure and activity in mouse brain models.

•  Mount imaging instruments on freely behaving mice and maintain animal health across longitudinal studies.

•  Implant and maintain cranial imaging windows in transgenic models that express multiple fluorescent proteins (e.g., Bitbow, Brainbow, glioblastoma models).

•  Execute and refine protocols for high-resolution, multiplexed fluorescence across multiple ROIs and imaging planes.

•  Assist in designing and validating optical elements and scan mechanisms, including random-access scanning with a microsystems scan mechanism.

•  Collect real-time 3D volumetric fluorescence data suitable for registration and quantitative analysis.

Image processing of multiphoton brain-imaging datasets

•  Process longitudinal multiphoton and complementary confocal 3D/4D fluorescence volumes of the same brain region imaged over time.

•  Develop, implement, and compare methods to register sequential 3D volumes (rigid, affine, and non-rigid / deformable).

•  Quantify rigid and non-rigid tissue displacement; estimate and correct motion from the animal, the microscope, and the tissue.

•  Establish objective metrics of registration accuracy and document failure modes (drift, photobleaching, intensity change, warping).

•  Segment fluorescent reporters or labeled structures and track them across sessions; distinguish true biological change from residual motion or registration error.

•  Apply computer-vision methods as needed, including state estimation, object tracking, segmentation, and 3D reconstruction.

•  Build reproducible analysis pipelines (preprocessing, registration, motion correction, segmentation, tracking, visualization) and contribute well-documented code.

Collaboration and scholarship

•  Collaborate with investigators in neuroscience, engineering, pathology, and the P41 Imaging Center on shared imaging and analysis goals.

•  Prepare figures, methods, and manuscripts; present results in lab meetings and at conferences.

•  Help translate working analysis methods into tools that other Center users can apply to their own datasets.

Qualifications

Required

•  PhD (or near completion) in Biomedical Engineering, Neuroscience, Computer Science, Electrical or Computer Engineering, Mechanical Engineering, Optical Engineering, Applied Mathematics, or a related field.

•  Evidence of independent research (first-author papers, substantial code or methods contributions, or equivalent).

•  Strong organizational, analytical, and problem-solving skills, and the ability to work across wet-lab and computational collaborators.

•  Excellent written and verbal communication.

Highly desirable — experimental

•  Hands-on experience with live-animal imaging (confocal, multiphoton, or epifluorescence microscopy).

•  Experience with rodent surgery, including cranial window implantation, and with maintaining animals through longitudinal imaging.

•  Familiarity with neuroscience models and genetically encoded fluorescent reporters (e.g., Bitbow, Brainbow, GCaMP).

Highly desirable — computational

•  Background in computer vision, state estimation, image registration, segmentation, object tracking, and/or 3D reconstruction.

•  Experience analyzing large 3D or 4D microscopy datasets, ideally multiphoton or other volumetric fluorescence imaging.

•  Working fluency in Python and/or MATLAB. Experience with ImageJ/Fiji, Napari, ANTs, elastix, ITK, Suite2p, CaImAn, TrackMate, or equivalent is a plus.

•  Comfort with version control, reproducible pipelines, and optionally GPU-accelerated or machine-learning approaches to image analysis.

Candidates need not check every box. We will consider experimentalists ready to grow on the analysis side, and computational scientists ready to work closely with in vivo imaging data.

Benefits and Research Environment

Competitive salary and benefits commensurate with experience and consistent with NIH postdoctoral guidelines; access to optical, surgical, and computational facilities, including the P41 Imaging Center and BSRB rooms D506 and D507; mentorship for careers in academia or industry; and a collaborative environment spanning Michigan Medicine and the College of Engineering. The Wang Laboratory occupies ~2,000 sq ft in the Biomedical Science Research Building (BSRB) on the Michigan Medicine campus, with 16 benches, desks, and computers. The lab is equipped for wet-lab and cell-culture work (4°C / −20°C / −80°C storage, centrifuges, laminar-flow hoods, CO2 incubators) and for optical imaging (brightfield and fluorescence microscopes). Specialized instrumentation includes an HPLC (Waters Breeze), an automated peptide synthesizer, and a lyophilizer. BSRB cores provide histology and an imaging laboratory with a Zeiss LSM 510 confocal (488, 514, 633 nm). An alarmed −80°C freezer room is adjacent to the core lab. The Center for Molecular Imaging supplies additional small-animal imaging systems and services. Computational work uses lab workstations plus University and P41 computing resources. P41 Imaging Center includes a dedicated microscope and imaging room, fit out with compressed air, scavenging and linear exhaust, laser-in-use controls, blackout, power and data, and bench services. Procedure room provides space for stereotactic cranial implantation and cranial-window surgery in support of longitudinal in vivo imaging.

How to Apply

Please send a cover letter, CV, contact information for three references, and a short statement of research interests to tdwangmd@gmail.com. Describe your experience with in vivo imaging, computational image analysis, or both, and note any work with multiphoton or other volumetric fluorescence datasets. Review begins immediately and continues until the position is filled. The University of Michigan is an equal opportunity employer.

Thomas D. Wang, MD,PhD

Professor of Medicine, Biomedical Engineering, Mechanical Engineering

H. Marvin Pollard Legacy Professor of Endoscopy Research

Director, National Center for Biomedical Imaging and Bioengineering (NCBIB)

109 Zina Pitcher Place, BSRB 1522

Ann Arbor, MI 48109-2200

Office: (734) 936-1228

Fax: (734) 647-7950

https://sites.google.com/a/umich.edu/wang_lab

https://sites.google.com/umich.edu/microendoscopy