Advanced Imaging and Microscopy Shared Resource

National Institute Of Biomedical Imaging And Bioengineering, Bethesda

Investigators

Linked publications, trials & patents

Abstract

The mandate of AIM is to operate, improve, and disseminate cutting-edge microscopy and image computation technology. Fiscal Year 2025 brought several improvements to AIM’s capabilities and operations. AIM brought onboard an additional Staff Scientist with a background in image computation to build and run computational pipelines utilizing artificial intelligence (AI) and high-performance computing. We completed the development of a new non-linear optical microscope that began its first user project. Our staff participated in collaborative and in-house innovation. As an important affiliated component of the newly formed BETA Center, and in fulfillment of our dissemination mandate, we organized, hosted, and conducted activities that promoted a more vibrant community of microscope builders both within and outside NIH. AIM’s principal function is as a collaborative resource for NIH researchers. During FY25, AIM collaborated on 37 projects with Principal Investigators from 11 NIH ICs and made acknowledged contributions to 6 accepted or published articles, and 8 manuscripts in preparation or submission. Notable developments and operational highlights not captured by our collaborators list and bibliography include: Resource Development Brian Lee, PhD joined AIM in December 2024 as an FTE computer scientist – bringing deep expertise in the use of traditional and artificial intelligence methods to perform advanced image processing and analysis including AI assisted segmentation and classification. The construction of a Coherent Anti-Stokes Raman Scattering (CARS)/2-Photon Microscope was completed in FY25. This microscope, operated by AIM for the BETA Center, brings new in vivo imaging capabilities to AIM – including conventional two-photon and second harmonic imaging, and extending to the more esoteric CARS imaging, which can image specific molecular vibrational bonds in live samples. While basic non-linear microscopy is widely used on the NIH campus for in vivo imaging, it has until now been missing from AIM’s portfolio. This CARS/2P microscope therefore represents an opportunity to extend AIM’s collaborative service to a new and large user base. This microscope has begun its first user project – a collaboration with Tobias Merson (NIMH) to image myelin in live brain tissue from a mouse model of diseases like multiple sclerosis that involve myelin degradation. The capabilities of our Single Molecule Microscope have been significantly enhanced. The field of view has been increased, a module has been added to enable spatio-termporally patterned photostimulation or photobleaching, and a strategy has been developed in collaboration with NCI to image and track single molecules in live animals. AIM microscopes, in particular the cleared tissue lightsheet microscope (CT-DISPIM) are producing ever greater volumes of image data. The CT-DISPIM can image centimeter-scale cleared tissue samples with sub-micron resolution – leading to data volumes that are massive (1-100TB). While acquiring this volume of data is challenging, it is the handling, processing, analysis, and visualization of these data that is the true limiting factor to generating biological insights. Recognizing this bottleneck, AIM has invested considerable effort into developing the hardware and software infrastructure to process terabyte scale image data. AIM has upgraded its local storage server from 0.8 petabytes (PB) to 3.7 PB. This server is located in the Building 35 data center, is managed by professional IT staff, and utilizes physical lift and shift data back-up to the cloud. Given that AIM stores and processes data for many user labs from multiple ICs, this upgrade is a critical component of a robust data handling strategy that protects NIH data integrity. As part of a 2024 NIH Director’s Challenge Innovation Award, AIM worked with collaborators at NCATS and NINDS to develop a user-friendly software platform for visualizing massive (>10TB) image data volumes. The software and data can be accessed via internet browser from any computer – enabling users to seamlessly navigate multi-terabyte image volumes from a remote desktop or laptop. Ongoing development will focus on adding the ability to perform manual or AI assisted segmentation, model training, testing, and deployment, all within the same platform. Dissemination AIM hosted an advanced imaging workshop organized by PAIR-UP (American Society for Cell Biology) who promote education and networking for imaging science trainees. AIM worked with NCI, NHLBI, and NIBIB to conduct this first ever PAIR-UP event at NIH which introduced 25 scientists from all over the US to advanced microscopy and computational methods. AIM’s work on a 2024 Director’s Challenge Innovation Award with collaborators from NCI and NIDDK was featured in an Emmy nominated PBS documentary titled “Shelter Me: The Cancer Pioneers”. AIM staff were invited participants at the 2024-2025 Nexus Workshop on “Enabling Access to Emerging Bioimaging Techniques” at Johns Hopkins University. This workshop brought together regional imaging experts to discuss mechanisms and strategies to make cutting-edge, pre-commercial imaging technology available to researchers. AIM helped to organize a quantitative microscopy summit between NIH and the National Institute of Standards and Technology (NIST). Optical microscopy labs at NIH met with NIST staff to workshop best practices for image quantitation, data traceability, and experimental reproducibility. AIM staff participated in a “hands-on” demonstration of NIBIB-built microscopy technology to roughly 50 Congressional Staff during an NIH visit sponsored by the American Institute for Medical and Biological Engineering (AIMBE).