Structure, Composition and Histology Core

Structure and composition across physiological length-scales (e.g., organ, tissue, cell, matrix, nanoscale-levels) are key intermediate traits that link gene expression with functional outcomes. Genetic and/or environmental perturbations affecting gene expression often lead to measurable changes in these intermediate traits that have mechanical and other functional consequences. Accurately quantifying structure and composition at different length scales is therefore essential to advancing our understanding of the molecular and mechanical mechanisms underlying musculoskeletal health and disease; to develop and evaluate treatment strategies; and to ultimately translate these strategies to the clinic. The Structure, Composition and Histology Core will provide access to the instruments and expertise that will enable Center investigators to quantify these intermediate traits and to accelerate their research programs.

Services include ex vivo and in vivo micro-Computed Tomography (CT) and ex vivo nano-Computed Tomography (nano-CT), Raman spectroscopy, and Histology as the major components.

The ex vivo microComputed Tomography (microCT) and nanoCT systems provide full 3-D reconstructed images of hard and soft biological tissues, as well as non-biological materials. The Dental School core has an ex vivo Scanco 100 microCT, and the Orthopaedic Research Laboratories ex vivo scanners are a GE Phoenix nanotom-m nanoCT and the in vivo scanner is a Bruker/Skyscan 1176 High Resolution micro-CT imaging system. See the websites listed below for details of system capabilities.

Raman spectroscopy services will be provided by Dr. Gurjit Mandair, who is located in the School of Dentistry. We provide guidance on sample preparation (fresh or embedded), compositional analysis (soft/hard tissues), and training on our Raman microscope/fiber-optic probe instruments

Histology is an essential component of all in vivo musculoskeletal studies. This core will enhance existing research by centralizing histologic efforts to achieve high quality and reasonably priced histology for center investigators, and to ensure, in collaboration with the other cores, a cost-effective, efficient, integrated, hierarchical approach to the evaluation of tissue phenotypes. Procedures are posted on the website.

The Histology part of this core supports these following procedures: plastic processing/embedding/sectioning and staining, paraffin processing/embedding/sectioning and staining, and frozen sectioning. Discounts are provided primarily for plastic procedures as the prices for paraffin procedures are very competitive with other facilities on campus.

An advanced histology training program has been developed to provide for the safe and proficient use of histological equipment. In addition to the training, supervision of first-time use is provided to be sure that all safety measures are being followed and the equipment is being used in the proper manner.

Each training session also comes with future technical support, slide Q & A, staining advice, etc., as our goal is to have trainees not just know how to produce histology products, but how to do it well and to understand what they are doing on a scientific level. Trainees are encouraged to ask our Histologists anything about the process, suggested processing adaptations, how to better prepare samples the next time, etc. We also have a stock of control tissue that is open for anyone completing the training.

Existing Core Websites:

Dental School microCT core: https://dent.umich.edu/research/microct-core

ORL nanoCT and microCT core: https://nanoctcore.med.umich.edu

ORL Histology core: https://histologycore.med.umich.edu (this site is under construction)

Contact: Contact David Kohn, PhD when beginning a project and for general assistance with core access. He will provide guidance on experimental design and the appropriate Faculty and Core expert to contact next.

Core Leadership

Services Offered and Prices

1. ex vivo/in vivo nanoCT and microCT: For P30 members, 20% of the cost for ex vivo nanoCT and microCT scanning is covered by the core center. Prices for the in vivo system are the same for P30 members and non-members. For more information to be trained to acquire scans or having small animals scanned in the in vivo scanner, contact Dr. Ken Kozloff (kenkoz@umich.edu).

The cost structure allows P30 members to choose the system based on scientific need rather than price.

2. See the Histology Workflow and Standard Operating Procedures (SOPs) for more information on the Cryosectioning, Paraffin and Plastic embedding and sectioning services. The various Workflow and SOPs describe the prep work, steps, and where each of the services listed below (items 3 & 4) would be involved in the process. Also available is a booklet containing all the protocols relative to plastic thin sectioning and histomorphometric analysis of the sections. Please note that plastic services extend the turnaround time due to extended processing times and the slow polymerization of the (poly) methyl methacrylate.

3. The Histology Core is using iLab to process histology requests. Requests for service may be submitted on the UMICH Orthopaedic Research Laboratories (ORL) Histology Core iLab page. Help or general information on using the iLab site can be found here.

4. Labor Rates for Miscellaneous Services

  • Plastic Services $52.00 / hour

  • Paraffin Services $37.60 / hour

5. Full Service Histology (services provided byMiMHC Core personnel; NOTE: Prices shown are effective 1/1/2022)

6. Self Service Histology (training provided by MiMHC Core personnel; only trained users can use sectioning equipment)

7. Advanced training (training provided by MiMHC Core personnel and includes the proper use of equipment, safety training, review of work, and quality assurance)

8. Additional equipment and services provided by the core:

  • Stratec XCT 2000 L peripheral quantitative computed tomography (pQCT) imaging system (training required)


  • Advice on use of Dragonfly software for image analysis, use of fully convolutional neural networks (FCNNs) for image segmentation, and development and validation of new FCNNs.


  • Advice on use of contrast agents and vascular perfusions to acquire 3D micro/nanoCT images of soft tissues


  • Access to Faxitron imaging in the Orthopaedic Research Laboratories

Referencing Core services in manuscripts

When referencing the use of the MiMHC Core services in your manuscripts, please use the following text:

"Research reported in this publication was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under Award Number P30 AR069620. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”