A Digital Atlas of the Guinea Pig Brain. A Comparative Study of qMRI at 3T with Histological Sections.

Marie Drottar (Boston University Division of Graduate Medical Sciences: BioImaging Program), Hernan Jara (Boston University Medical School Department of Radiology)


High quality magnetic resonance images of the guinea pig brain have been collected using quantitative MRI scanning techniques. This series of images reveals a set of digital images of the guinea pig brain in sections that are comparable to a set of images obtained with commonly used histological sectioning and staining protocols. These image sets lend themselves to the construction of a freely accessible and user friendly digital atlas that can be labeled with anatomical structures and used as a searchable database.


One healthy adult male guinea pig was sub-lethally anesthetized and perfused with 4% formalin through the heart in accordance with the IACUC approved protocol at the Mass Eye and Ear Infirmary. The entire brain (still within the cranial vault), was post-fixed for 2 hrs in 4% formalin, and then removed into 0.01M phosphate buffered saline for one week. The specimen was then immobilized in a 2% agarose block.  Imaging was accomplished using a z3D-mixed-TSE scanning protocol in a 3T clinical MRI scanner (Philips Medical Systems, Cleveland OH). After Scanning was accomplished, the specimen was removed from agarose, dissected from the cranial vault, and frozen sectioned at 80um on a sliding microtome. Alternate sections were stained with a Nissl stain, and an acetylcholinesterase  stain.


Three sets of anatomical images were converted to jpeg format, and multiple anatomical structures were labeled in order to make comparisons.


The quantitative magnetic resonance images (qMRI)  provide an anatomical image set which is comparable to the pervasive “gold standard” histological data. These image sets lend themselves easily to the construction of digital image sets which will be accessible, searchable and forms a valuable resource to the research community. This pulse sequence and construction format also has the potential to be applied  to  in vivo applications.

Preferred presentation format: Poster
Topic: Digital atlasing

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