Histology Lab Service Core

The Histology Core at Indiana University School of Medicine–Indianapolis provides histological services for basic science (non-clinical) research. Both mineralized (plastic embedded) and soft tissue (paraffin embedded) specimens can be prepared by the facility. This lab is part of the Bone and Body Composition Core of the Indiana Clinical Translational Sciences Institute (CTSI) and is also a core facility of the Indiana Center for Musculoskeletal Health. This core laboratory is directed by David Burr, PhD.


The Histology Core provides standard histological preparation, histomorphometric analysis and interpretation to investigators working in a variety of areas, including studies of bone, cartilage, cancer, pancreas, kidney and brain. The core also provides quality assurance and standard operating procedures (SOPs) for all analytical methodology used for histologically related analyses. The Core directors and its faculty have worked together for many years, demonstrating fully established and mature collaborative relationships.

The laboratory processes, embeds, sections and stains decalcified and undecalcified tissues for nearly 100 different individual laboratories within the Indiana University School of Medicine and broader Indiana University system, and for other laboratories in the United States. The facility processes between 8000 and 9000 specimens per year. This is one of the few laboratories on the IU School of Medicine–Indianapolis campus that can process large quantities of material because of our automatic processing capabilities.

Plastic (methyl methacrylate) Embedding and Sectioning Service

This research facility offers processing of specimens through plastic (methyl methacrylate; MMA) embedding as well as thick sectioning of cortical bone, thin sectioning of trabecular (cancellous) bone, and staining of plastic sections.

The facility provides cover-slipped unstained sections for analysis of fluorochromes (dynamic histomorphometry) at no charge. Specialized stains (for static histomorphometry) are available. Goldner’s Trichrome (GT; osteoid, osteoblasts and osteoclasts), Hematoxylin and eosin (HE; routine assessment) and Toluidine Blue (TB; cement lines and cartilage) are available for both thick and thin sections. Tartrate-Resistant Acid Phosphatase (TRAP; osteoclasts) and Von Kossa / MacNeal (VKM; osteoid, osteoblasts and osteoclasts) are available for thin sections only.

Paraffin Embedding and Sectioning Service

The Histology Core offers de-mineralization of mineralized tissue (if necessary), processing of specimens through paraffin embedding, thin sectioning of paraffin-embedded tissue, and staining of paraffin sections.

For routine assessment, slides are stained with hematoxylin and eosin (HE; Harris hematoxylin, regressive method). Specialized stains are available, including Acidified Toluidine Blue (AcTB; for mast cells); Fast Green – Safranin O (FG/SO; for cartilage); Gomori’s Aldehyde Fuchsin, Wenk Modification (GAF; for pancreatic β cells, elastin, mast cells); Jones’ Periodic Acid-Silver Methenamine, AFIP Modification (JPA-ArM; for kidney glomerular capillary basement membrane); Masson’s Trichrome (MT; for collagen); Oil Red O (ORO; for lipids); Periodic Acid Schiff Procedure (PAS; for carbohydrates); Perls Iron Stain (PI); Tartrate-Resistant Acid Phosphatase (TRAP; for osteoclasts); Verhoeff-Van Giesen (VVG; for elastin); and Von Kossa Method for Mineral (VK).


Materials for processing can be dropped off on the bench opposite the lab door (MS-5045G). All submissions require a completed work order form.

Formalin-fixed tissue for either plastic or paraffin embedding should be submitted immersed in 70 percent ethanol (EtOH), not formalin. Specimens not submitted in histology cassettes will be charged for cassettes, if appropriate.

N.B. Cassettes must be labeled with either pencil or solvent-resistant markers as listed below. Labeling done with Sharpies® or similar ink pens comes off during processing. Approved marking pens include Cancer Diagnostics Moist Marker Plus from Lab Safety Supply, HistoPrep Pen from Fisher Scientific, Klinipath KP Marker Plus from Mercedes medical, and Stafmark Pen from Statlab Medical Products.

Blocks for re-cutting and slides for staining can be submitted as is. The designated contact person will be notified by email when the work order is complete. For questions concerning submissions, email Keith Condon.

Histology Core Work Order Forms



Pricing information is available for IU School of Medicine investigators as well as outside investigators.


Investigators using the services and equipment provided by the IU School of Medicine at the Histology facility should review facility policies on confidentiality, sample removal and more.


The Histology Core observes protocols for specimen fixation, demineralization, paraffin embedding and sectioning, and plastic embedding and sectioning.