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National Institutes of Health

Eunice Kennedy Shriver National Institute of Child Health and Human Development

2022 Annual Report of the Division of Intramural Research

NICHD Microscopy and Imaging Core

Vincent Schram
  • Vincent Schram, PhD, Acting Executive Director
  • Tamás Balla, MD, PhD, Scientific & Administrative Director
  • Ling Yi, PhD, Staff Scientist
  • Louis (Chip) Dye, BS, Research Assistant

The mission of the NICHD Microscopy and Imaging Core (MIC) is to provide service in four different areas: (1) histology and sample preparation for light and electron microscopy; (2) wide-field and confocal light microscopy; (3) transmission electron microscopy (TEM); and (4) image analysis and data extraction. The Facility operates as a ’one-stop shop,’ where investigators can, with a minimum of effort, go from their scientific question to the final data.

Mode of operation

Located on the ground floor of the Porter Building (building 35A), the MIC is accessible 24/7, and users can reserve time on each microscope by using an online calendar. The facility is available free of charge to all NICHD investigators and, resources allowing, to anyone within the Porter building. The facility is supported by the Office of the Scientific Director, NICHD. The MIC is under the joined management of Tamás Balla (Scientific and Administrative director) and Vincent Schram (acting executive director).

Schram is the point person for light microscopy and data analysis. Ling Yi is in charge of the histology/sample preparation unit. The Electron Microscopy (EM) branch of the Facility is staffed by Chip Dye. Ling Yi and Chip Dye report to Vincent Schram, who coordinates activities with Tamás Balla.

The MIC has an open-door policy with the NINDS Light Imaging Facility (LIF, Building 35). The two cores freely exchange users, share equipment, and trade support. Although not officially sanctioned, this mode of operation provides extended support hours, wider expertise, and access to more equipment than each Institute could afford on its own.

The MIC serves over 300 registered users in 68 laboratories. NICHD uses 80% of the facility's resources, NINDS 15%, and other Institutes (NIBIB, NIA, and NIMH) the remaining 5%.

Light microscopy

The MIC is equipped with six confocal microscopes, each optimized for certain applications: (1) A Zeiss LSM 710 inverted for high-resolution confocal imaging; (2) the Nikon Spinning Disk/Total Internal Reflection Fluorescence (TIRF), equipped with advanced rotating TIRF capabilities; (3) a Zeiss LSM 880 2-photon confocal for thick tissues and live animals; (4) a Zeiss 800 optimized for advanced tiling experiments; and (5) a Zeiss 880 AiryScan with higher spatial resolution. The older Zeiss LSM 780 was retired in July 2022 and replaced with a modern LSM 900 equipped with an AiryScan detector.

The fully automatic Zeiss Axioscan Z1 slide scanner was heavily used in FY 2022, freeing up hundreds of personnel hours for several research units in the DIR. We also installed a high-end wide-angle fluorescence microscope to complement our equipment base for non-confocal microscopy imaging.

High-end computer workstations with imaging software (Zeiss Zen, Nikon Elements, Bitplane Imaris, SVI Hyugens and ImageJ) continue to be used for data extraction. Unfortunately, the MIC began to be handicapped by acute network connectivity issues in June 2022, a problem that shows no sign of being resolved.

The light microscopy branch of the MIC continues to rely on the same mode of operation. After an initial orientation, during which their project is researched by the staff and the best approach is decided upon, users receive hands-on training on the equipment and/or software best suited to their goals, followed by continuous support when required. Once image acquisition is complete, the staff devise solutions and train users on how to extract usable data from their images.

Electron microscopy

The electron microscopy section of the facility processes specimens from start to finish: fixation, embedding, semi-thin and ultra-thin sectioning, staining, and imaging on the JEOL 1400 transmission electron microscope. Because of the labor involved, the volume is necessarily smaller than for the light microscopy branch, in which end users perform their own processing and imaging. In the past 12 months, Chip Dye processed a total of 148 samples for morphology studies.

An automatic sample preparation device from Microscopy Solutions was acquired and installed, allowing the volume of specimens processed to be increased. John Heuser, an expert in electron microscopy, continues to use the JEOL 1400 microscope and interface with Chip Dye, who brings his extensive experience to the MIC.

Tissue preparation

The histology/sample preparation lab is the cornerstone of the MIC. Ling Yi has done a remarkable job to ensure a smooth transition after Lynne Holtzclaw's departure, and is now providing sample processing and histology services for light and electron microscopy.

Twenty-two users were trained in-person in rodent perfusion, cryopreservation, cryosectioning, immunofluorescence, and RNAscope. Perfusion and cryosectioning services were provided to eight laboratories. NICHD users include Andres Buonanno, Rena D'Souza, Douglas Fields, Dax Hoffman, Claire Le Pichon, Karl Pfeifer, and Brant Weinstein. Users from other Institutes include Paule Joseph (NIAAA) and Mario Penzo (NIMH).

Ling Yi invested heavily in implementing RNAscope applications in the MIC, to the point where it has become routine for many of the facility's users. She is currently working on optimizing tissue clearing methods by shortening the long incubation times these techniques require.

Image analysis

High-end computer workstations with imaging software (Zeiss Zen, Nikon Element, Bitplane Imaris, SVI Hyugens, and ImageJ) are available at the MIC.

Image processing based on neural networks (Artificial Intelligence or AI) is a remarkably powerful tool for image restoration, segmentation, and resolution improvement. The MIC is actively looking into AI–powered solutions for image restoration and segmentation. The Nikon NIS-AI suite, an advanced software for noise removal and segmentation not possible with conventional methods, is available in the Core.


  • John Heuser, PhD, Section on Integrative Biophysics, NICHD, Bethesda, MD
  • Carolyn L. Smith, PhD, Light Imaging Facility, NINDS, Bethesda, MD


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