Wednesday, January 7, 2026 1/7/2026

Groundwork for a Synchrotron MicroCT Imaging Resource for Biology (SMIRB)

Award Number: R24OD018559
ORGANIZATION: OFFICE OF THE DIRECTOR, NIH
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/15/2015
PERIOD OF PERFORMANCE END DATE: 07/31/2025

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Groundwork for a Synchrotron MicroCT Imaging Resource for Biology (SMIRB) - Project Summary Each major human disease is associated with a specific range of morphological changes to cells and tissues in the micron scale. Normal and abnormal structure was discovered and is still characterized using histology - a microscopic technique that depends on physical tissue slices. Presently, histology’s use in systems biology is limited by its largely descriptive and two-dimensional nature. Making histology quantitative and three-dimensional would be potentially transformational for research and diagnostics, but has been impractical. Accordingly, we have now created a 3D form of histology by customizing X-ray microtomography (micro-CT) of fixed and stained, millimeter-scale, whole organisms and tissue samples. We used fixed and metal-stained, whole zebrafish because they contain a full range of tissues within the size range currently studied histologically. The result is the first practical way to create virtual histology-like “sections” in any plane. Three-dimensional, complete histological phenotyping has potential use in genetic and chemical screens, and in clinical and toxicological tissue diagnostics. Here, we propose the next steps needed to enable high-throughput, quantitative, 3D histological phenotyping of whole, millimeter-scale animals. The proposed work applies the principles of chemistry, physics, and computer science to improve image resolution, throughput, and analytics, organized into three specific aims. Specific Aim 1 will build on our developments in this project and further improve imaging volume and resolution by upgrading imaging array, optics, and sub-pixel shifting, and to throughput by changes in sample embedding, loading geometry and mechanics, helical CT scanning, scintillator material, and to data sharing by improvements to the ViewTool infrastructure and user interface. Specific Aim 2 will yield reference images to define the range of normal phenotypic variation and to obtain samples related to a range of potential applications. Specific Aim 3 will apply the power of machine learning to segmentation, annotation, and analytics. Together, this work will establish a practical foundation for large-scale genetic and chemical screens involving mm-scale, whole organisms based on 3-dimensional, quantitative, histological phenotyping. The instrumentation and analytics will be state-of-the-art in its combination of resolution, field-of-view, pancellularity, image quality, analytical potential, throughput, sample stability, and reproducibility and largely usable with both tube and synchrotron X-ray sources. The voxel resolution will be at least 0.5 μm across fields-of-view of up to 1 cm. Representation of every cell type make the images suitable for cross-referencing across imaging modalities. Potential applications will be explored, “wild-type” will begin to be defined, and training sets for automated segmentation generated. The potential impact will encompass the missions of most NIH Institutes and Centers. The whole-animal genetic and chemical screens enabled are expected to impact drug development, diagnostics, and our basic understanding of how genes and environment define phenotype.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = -$4,299 )
2026	2022	PENNSYLVANIA STATE UNIVERSITY	500 UNIVERSITY DRIVE	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	8	12/12/2025	NON-COMPETING CONTINUATION	-$4,299
														Subtotal = -$4,299

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2022	PENNSYLVANIA STATE UNIVERSITY	500 UNIVERSITY DRIVE	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	8	8/15/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $978,502 )
2022	2022	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	003	8	7/28/2022	SUPPLEMENT FOR EXPANSION	$231,489
2022	2022	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	7	4/30/2022	SUPPLEMENT FOR EXPANSION	$25,648
2022	2022	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	002	8	7/27/2022	SUPPLEMENT FOR EXPANSION	$78,848
2022	2022	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	001	8	7/26/2022	NON-COMPETING CONTINUATION	$642,517
														Subtotal = $978,502

Issue Date FY: 2021 ( Subtotal = $803,921 )
2021	2021	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	7	7/23/2021	NON-COMPETING CONTINUATION	$657,323
2021	2021	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY AVE RM C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	001	7	8/18/2021	SUPPLEMENT FOR EXPANSION	$146,598
														Subtotal = $803,921

Issue Date FY: 2020 ( Subtotal = $1,310,965 )
2020	2020	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	002	6	7/23/2020	NON-COMPETING CONTINUATION	$655,482
2020	2020	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	003	6	8/1/2020	SUPPLEMENT FOR EXPANSION	$655,483
2020	2019	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	001	5	3/10/2020	COMPETING CONTINUATION	$76,539
2020	2018	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	4	3/10/2020	NON-COMPETING CONTINUATION	-$76,539
														Subtotal = $1,310,965

Issue Date FY: 2019 ( Subtotal = $667,280 )
2019	2019	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	001	5	8/8/2019	COMPETING CONTINUATION	$667,280
2019	2018	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	4	8/8/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $667,280

Issue Date FY: 2018 ( Subtotal = $654,197 )
2018	2018	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	4	8/11/2018	NON-COMPETING CONTINUATION	$654,197
														Subtotal = $654,197

Issue Date FY: 2017 ( Subtotal = $639,616 )
2017	2017	PENNSYLVANIA STATE UNIVERSITY, THE	500 UNIVERSITY DR C1607	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	3	8/25/2017	NON-COMPETING CONTINUATION	$639,616
														Subtotal = $639,616

Issue Date FY: 2016 ( Subtotal = $671,672 )
2016	2016	MILTON S HERSHEY MEDICAL CENTER	500 UNIVERSITY DRIVE, POB 850	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	2	7/20/2016	NON-COMPETING CONTINUATION	$671,672
														Subtotal = $671,672

Issue Date FY: 2015 ( Subtotal = $651,243 )
2015	2015	MILTON S HERSHEY MEDICAL CENTER	500 UNIVERSITY DRIVE, POB 850	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	000	1	7/17/2015	NEW	$666,726
2015	2015	MILTON S HERSHEY MEDICAL CENTER	500 UNIVERSITY DRIVE, POB 850	HERSHEY	PA	17033	DAUPHIN	USA	Research Infrastructure Programs	001	1	9/10/2015	NEW	-$15,483
														Subtotal = $651,243

Grand Total All Awards = $6,373,097

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Groundwork for a Synchrotron MicroCT Imaging Resource for Biology (SMIRB)

Award Number: R24OD018559

ORGANIZATION: OFFICE OF THE DIRECTOR, NIH

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 08/15/2015

PERIOD OF PERFORMANCE END DATE: 07/31/2025

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