Neuropathology Core

Neuropathology Core

Neuropathology Core

The major functions of the Neuropathology Core are as follows:

  • Collect, store and characterize human TBI and control specimens for research in military TBI.
  • Provide tissue processing, staining, and slide digitizing.
  • Maintain state-of-the-art histopathology laboratories designed specifically to separately handle human and animal brain tissue specimens.  
  • Maintain a detailed computerized inventory system of all specimens.
  • Process requests and disbursements of samples to approved researchers.  


The Neuropathology Core is an academic research-oriented component of CNRM. The Neuropathology Core is located at an off-campus facility and is fully equipped with state-of-the-art facilities and expertise for various types of neuropathologic research and translational activities. The facility has been organized to optimize laboratory certifications, freezer operations, and storage.

Histopathology Resources and Services at USU

CNRM provided equipment to the Neuropathology Core to increase the quality and capacity of processing and slide preparation of fresh-frozen and paraffin-embedded nervous system tissues. Investigators can contact the Neuropathology Core to ask about the possibility to collaborate for research purposes with the Core.

The Neuropathology Core has the following equipment and instruments available:

Virtual Pathology:

  • Nanozoomer digital pathology ("Virtual Microscopy") system. This system is capable of digitizing brightfield slides, store and share images for multiple diagnostic and research purposes and qualitative-quantitative studies. Digitizing slide preparations allows more efficient image capture than standard microscopy and enables use of image analysis tools purchased to support the Nanozoomer system.
  • BrainMaker Software. This program is capable of organizing, redefining, and re-constructing serially-organized slides sequences in 3D and creates movies of the final 3D output/image for a better visualization of the normal vs. pathologic conditions.

Digitalized Image Storage:

  • Biolucida Platform Biolucida is software for managing large amounts of digitized images such as high-resolution image montages, 2D and 3D image data and more.

Quantitative Neuropathology:

  • StereoInvestigator for unbiased stereology. This sophisticated system for neurohistological quantification providing accurate, unbiased estimates of the number, length, area, and volume of cells or biological structures in a tissue specimen. It is a key research tool that has helped lead advances in numerous areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior.
  • Neurolucida system and Neurolucida 360. This software and hardware assists researchers with digital reconstruction of images that can then be morphometrically analyzed to understand more about neuronal structure. Data can be obtained about somas, dendrites, axons, spines, and synapses to examine an experimental hypothesis. The entire neuron can be traced to develop a complete digital neuron reconstruction for quantitative and qualitative analysis.


  • 2 Fully-automated Tissue Processor Machines
  • 2 Automated Staining Systems, BOND (separately dedicated to animal and brain tissue)               
  • 4 Automated microtomes
  • 2 cryostat (separately dedicated to animal and human brain cutting)

Brightfield Microscopy:

  • Zeiss, ImagerA2
  • Zeiss ImagerA2
  • Olympus 1
  • Olympus 2

Human Neuropathology Resources/ Expertise

Resources for cutting and staining human brain specimens: A Nanozoomer HT system with low magnification and high throughput capacity is available to generate high quality digital images of stained specimen images. This digitizing system is used with applications of image analysis software for qualitative and quantitative neuropathological analysis. Digitized images are designed to maximize collaborative use of the specimens, which will facilitate the research programs across investigators. A team of histotechnologists oversees the human and animal specimen processing for approved CNRM studies.

CNRM Brain Tissue Repository (BTR)

Human brain donation is one of the most generous gifts and valuable contributions to neuroscience and medical research in general, especially studies of traumatic brain injury (TBI) and TBI-related neuropsychiatric consequences. Approximately 15–20% of service members returning from combat zones reported having had at least one TBI during their tours of duty as well as post-traumatic stress disorder (PTSD).  Data suggest that a higher percentage of recently deployed service members have suffered from TBIs, including single TBI, repetitive TBI, and blast-TBI. Unfortunately, little is known about how the brain is damaged following a TBI and if PTSD is associated with distinct neurobiological and pathologic processes related to specific type of TBI as well. In response, the CNRM has established a Brain Tissue Repository (BTR) to which the families of deceased service members, veterans, and other eligible donors, including civilians, may contribute. Through the gift of brain donation scientists will be able to conduct research on many aspects of TBI which promised to lead to the identification of causes and possible treatments for the short- and long-terms neuropathologic consequences of TBI and TBI-related illnesses.

Points of contact for information on core resources, policies, and procedures

Dr. Daniel Perl, Director, Brain Tissue Repository and Neuropathology Core,

Dr. Diego Iacono, Deputy Director, Brain Tissue Repository and Neuropathology Core,


CNRM Brain Repository, 855-DON8-TBI (855-366-8824) or

 Access to CNRM core resources is available for CNRM funded studies and for broader research needs according to CNRM policies, including prioritization and cost sharing.  For further information about the policies or for a copy, please email