Tissue Pathology & Biospecimen

The Tissue Pathology & Biospecimen Shared Resource (TPB SR) at Stephenson Cancer Center (SCC) provides services in two areas central to basic, translational, and clinical cancer research – specifically tissue pathology and biospecimen collection and annotation. The TPB SR is led by a board-certified pathologist, Kar-Ming Fung, M.D., while the tissue pathology and biospecimen services have their own respective team leaders.

Tissue Pathology Service

The Tissue Pathology Service provides:

  • Consultation on experimental design and assistance with interpretation of histopathology and staining results
  • Conventional histology services including tissue decalcification, processing, and embedding (paraffin and frozen); paraffin and frozen sections; and conventional staining such as hematoxylin-eosin, trichrome, Sirius red, PAS, Giemsa, and Luxol Fast Blue among others
  • Construction of tissue and cell microarray(s) (TMA/CMA)
  • Automated molecule-specific staining including single or multiplex immunohistochemistry (IHC), immunofluorescence (IF), chromogen and fluorescence-based in situ hybridization (ISH-C, ISH-F); combined IHC-ISH-C/IF-ISH-F; and TUNEL
  • Bright-field and fluorescence-based (up to 7 channels) whole slide scanning up to 40x with image analysis software
  • Bright-field, polarized light, and fluorescence single-frame digital photography
  • Size-based collection of tumor cells using Rarecell ISET and laser capture microscopy

For IHC, IF, ISH-C, & ISH-F, investigators must provide the primary probe; the TPB SR will provide the detection system and all other required materials, including assistance with appropriate positive and negative controls. Whole slide scanning, image analysis, digital photography, and laser capture microscopy are essentially self-service following completion of training. Frozen sectioning can be either self-service or staff-operated. Other services are provided by TBP SR staff.

The full-service brochure is available here.

The Tissue Pathology Service has the following equipment available for specific services:




Conventional Histology

ST5020 stainer, TP 2010 processing machine, EG1150H embedding center, CM1950 cyrostat, R2255 microtome, Brady BSP31 cassette labeler, BBP11 label marker, Zeiss microscope.

Histologic processing, embedding, sectioning (frozen & paraffin blocks). Equipment is staff operated except for the cryostat which trained researchers may operate.

Tissue/Cell Microarray

Veridiam 110c TMA manual arrayer.

Construction of tissue/cell microarray(s) (TMA/CMA). Equipment is staff operated.

Cell/Tissue Isolation

Thermofisher Cytospin 4, Leica LMD7 laser capture microscope, and Rarecell ISET.

Isolate tumor cells. The Rarecell ISET is staff operated. The cytospin and laser capture microscope may be self-operated by trained researchers.

Automated IHC, IF, ISH, TUNEL

Leica BOND III & BOND RX automated stainers with multiple antigen retrieval protocols & flexible IHC/IF programs.

Automated staining. Equipment is staff operated. Both machines have capacities of 30 slides per run. ISH using kits from ACD can only run on the BOND RX.

Whole Slide Scanning

Zeiss AxioScan.Z1 whole slide scanner(capacity is 100 standard slides; 2x and 4x sized slides can also be scanned) & Zeiss physical server (.czi file format). Leica-Aperio CS whole slide scanner (capacity 5 standard slides) & Aperio virtual server (.svs file format) with file management software.

Whole slide scanning. The Zeiss scanner has both bright-field & fluorescence scanning (up to 7 channels), while the Leica-Aperio scanner is bright-field scanning only. Both can scan up to 40x with numerical aperture at 0.95 (Zeiss) and 0.75 (Leica-Aperio) respectively. Both scanners are self-operated by trained researchers; staff assisted scanning is available as needed. Overnight scanning and weekend access are routinely available.

Image Analysis

Indica HALO Plus 101 and Leica-Aperio2 image analysis software.

Image analysis. Self-operated. Leica-Aperio software is available online. HALO is loaded on laptops.

Laptops for Image analysis

Three laptops each loaded with a site license of HALO Plus 10.

Self-operated laptops available for loan. Leica-Aperio ImageScope is also loaded on these laptops.

Photomicrography & Figure Assembly

Nikon Eclipse Ni-E microscope & camera, Adobe Photoshop.

Bright-field and fluorescence (up to 3 channels) digital photomicrography. Both are self-operated after training. Staff assisted figure construction is available.

1 Algorithms of HALO Plus 10 include area quantitation, tissue classifier, tissue microarray (TMA), spatial analysis, ISH-IHC, immune cell, cytonuclear quantitation FL, high-plex FL, membrane quantitation FL, membrane IHC quantitation, and cytonuclear IHC quantitation. 2 Algorithms of Leica-Aperio image analysis software include positive pixel count, membrane count, vessel count, nuclear count, cytoplasmic count, rare event count, color deconvolution, ISH quantitation, and TMA segregation.

Biospecimen Service

The Biospecimen Service provides:

  • Prospective and retrospective specimens annotated with demographics, pathological diagnosis, staging, biomarkers and clinical information
  • Procurement for prospective specimens
  • Retrieval of archival materials
  • Storage of human specimens including tissue, blood and other specimen types as required
  • Distribution of fresh, frozen and paraffin-embedded specimens to approved investigators
  • Liaison between investigators and the Department of Pathology regarding search and retrieval of archival materials
  • Consultation between pathologists and researchers for protocol development and specimen evaluation

Type and availability of samples differ by organ; a web-based catalog of annotated specimens is available. Permission to access the catalog can be obtained through the TBP SR office. The biospecimen bank currently contains over 30,000 aliquoted samples collected since 2008, including tissue, blood, plasma, serum, cell and buccal samples. The Biospecimen Service utilizes an IRB-approved Universal Consent that allows patients at OU Health to donate tissue or blood; over 3,500 patients have consented to participate since 2008. The collection contains especially large numbers of gynecologic and pancreatic cancer specimens.

If relevant specimens are not available in the Biospecimen Bank, staff will facilitate the procurement of specimens from appropriate sources, including archival samples stored within the Department of Pathology. Staff also support protocol-driven specimen collection for specific research projects. Users are encouraged to contact the Biospecimen Service for more information.

Access TPB SR Services

To request any TPB SR service, visit the iLab page. You may need to set up an account when you visit iLab for the first time. Within iLab, you can request services, monitor progress of your project, and communicate with TBP SR staff.

Contact Information

Biospeciman Acquisition Core and Bank
P: (405) 271-1688
E: scc-biospecimen-core@ouhsc.edu

Tissue Pathology Service
Muralidharan Jayaraman, Ph.D.
Director of Research Core Operations
P: (405) 271-8001 x 30492
E: Muralidharan-jayaraman@ouhsc.edu
Main Facility
Floor 4, Biomedical Research Center (BRC)
OU Health Sciences Center
Satellite Facility
Floor 3, Stephenson Cancer Center
OU Health Sciences Center
This location supports the phase I clinical trials program.


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