Figure 3.

Retrosplenial and hippocampal–parahippocampal connectome. The connectome (see ratbrain_connectome.pdf in Supplementary Material) consists of 14 large, color-coded boxes, which represent the sub-regions of the hippocampal formation, parahippocampal region, and retrosplenial cortex. In this figure, the user interface elements of the connectome are indicated with color-coded outlines and their meaning/purpose is explained. (A) In the white outlines, the 14 anatomical sub-regions are displayed. (B) The 14 anatomical sub-regions are three-dimensionally organized. However, the origin and termination of connections are not always described in full detail in the literature. Therefore, area boxes are divided into four quadrants. Quadrant I has full topological information, whereas the other quadrants have less topological detail. In quadrant I, the vertical axis in the connectome represents the septotemporal axis of dentate gyrus (DG), Cornu Ammonis (CA3 and CA1), subiculum (Sub), presubiculum (PrS) and parasubiculum (PaS), and the dorsoventral axis of medial and lateral entorhinal area (MEA and LEA), retrosplenial cortex (A29 and A30), perirhinal cortex (A35 and A36) and postrhinal cortex (POR). The sidebars (B) display the dorsoventral and septotemporal axes of the anatomical sub-regions. The horizontal axis within quadrant I and III represents the proximodistal axis in CA3, CA1, Sub, PrS, and PaS; the rostrocaudal axis in A29c, A30, A35, A36, and POR and the DG is subdivided into the inner/outer blades and crest region. Within the area boxes, the layers for each specific subarea are outlined. In quadrant II, the information of the vertical axis and the layers are specified, but no details of the horizontal axis are presented. In quadrant III the horizontal axis and the layers are represented, while in quadrant IV, only layer information is present. (C) The interactive connectome allows visualization of detailed connectivity patterns within and between sub-regions. To search for connections, use the search button on the toolbar (C). The toolbar has eight buttons (from left to right): Search for connections, show all connections, clear all connections, a short tutorial on how to search for connections, a help section, contact information, a link to the project website www.temporal-lobe.com and information about how to support this project. (D) If the toolbar is closed, clicking the “open toolbar” button will restore it. (E) After a search is carried out, the retrieved connections will be drawn in the diagram between the appropriate areas and quadrants. Additionally, an eye-icon will appear in the layers panel on the left (E). This is an alphabetically sorted list of “from → to” connection groups that can also be switched on or off manually. In front of each group is a “+” icon. Clicking this icon expands the list of individual connections that make up the group, allowing one to select connections originating from a specific cortical layer or according to a specific three-dimensional projection pattern. (F) The figure panel provides a detailed anatomical description of the retrosplenial cortex, the hippocampal formation and the parahipppcampal region, together with translation tables for nomenclature. Use the buttons in this panel to switch between the figures.