Digital Atlas of Anatomical Subdivisions and Boundaries of the Rat Hippocampal Region

Abstract

The rat hippocampal region is frequently studied in relation to learning and memory processes and brain diseases. The region is complex, consisting of multiple subdivisions that are challenging to delineate anatomically. Published atlases of the rat brain typically lack the underlying histological criteria necessary to identify boundaries, and textbooks descriptions of the region are often inadequately illustrated and thus difficult to relate to experimental data. An overview of both anatomical features and criteria used to delineate boundaries is required to assign location to experimental material from the hippocampal region. To address this issue, we have developed a web-based atlas application in which images of histological sections are integrated with new and up-to-date criteria for subdividing the rat hippocampus formation, fasciola, and associated parahippocampal regions. The atlas application consists of an interactive image viewer with high-resolution images of an extensive series of sections stained for NeuN, calbindin, and parvalbumin, and an index of structures with detailed descriptions of the criteria used to define the boundaries. Images can be inspected with a graphical overlay of selected subregions. Bi-directional links between images and the index of structures are provided. In summary, we provide a novel content-rich digital atlas resource facilitating identification of morphological features relevant for delineating the anatomical subdivisions of the rat hippocampal region. The atlas application is available at .

Hippocampal Formation

“…For further details on the cytoarchitectonic organization of the PrS as well as the description of several characteristics of the PrS that help to differentiate it from the PaS the reader is referred to studies by Haug (1976), Van Groen and Wyss (1990a) Insausti et al (1997) and Kjønigsen et al (2011).…”

“…In the following section, we will discuss the position, laminar organization and cytoarchitectonics of the PHR areas presubiculum (PrS), parasubiculum (PaS), medial and lateral entorhinal cortex (MEC and LEC), perirhinal cortex (PER) and postrhinal cortex (POR). Our cytoarchitectonic descriptions follow the nomenclature as defined in Kjønigsen et al (2011) and Boccara et al (2014).…”

Voxelized Model of Brain Infusion That Accounts for Small Feature Fissures: Comparison With Magnetic Resonance Tracer Studies

“…These regions were clearly seen as dark regions on GA maps and fissures could be traced out manually within the hippocampus. Fissure and CSF regions were also checked by comparing them to a rat atlas [38,39]. Figure 2(b) shows segmentation of fissures in the dorsal and ventral hippocampus based on GA.…”

“…GA values were then used to segment WM and GM in these regions. Thresholds for AD, FA, and GA were adjusted using visualization software (AMIRA v.4.1, TGS, San Diego, CA) and determined by making segmented regions match a rat brain atlas [38,39]. Final threshold values are listed in Table 1.…”

The use of manganese-enhanced MRI for the evaluation of neurodegenerative changes in a rat model of kainic acid- induced excitotoxicity

“…(ROIs). ROI analyses were performed on both injected (ipsilateral) and contralateral sites of rats treated with KA and saline (11).…”