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The connectome manual slide show.


The nitty gritty manual

The tabs below contain a guide to different aspects of working with the diagram. In case you do not find what you were looking for, please log in to the website and ask your question in the forum.

Figure 1: The Connectome



  1. Quick Start
  2. Area boxes
  3. 3D position
  4. Area boxes: details
  5. Toolbar
  6. Searching Connections
After opening the connectome in Acrobat Reader, a view similar to the image above should be visible on your computer screen. This first section in the manual provides a quick overview of the connectome. The connectome 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 8 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 menu’ 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.
The connectome canvas (figure 1, white outline) consists of 14 large, color-coded area boxes, which represent the sub-regions of the hippocampal formation, parahippocampal region and retrosplenial cortex. To keep the connectome orderly, area names are abbreviated. The areas included are:

Hippocampal formation:

  • Dentate gyrus (DG)
  • CA3
  • CA1
  • Subiculum (Sub)

Parahippocampal region:

  • Presubiculum (PrS)
  • Parasubiculum (PaS)
  • Lateral Entorhinal Area (LEA)
  • Medial Entorhinal Area (MEA)
  • Perirhinal cortex Area 35 (A35)
  • Perirhinal cortex Area 36 (A36)
  • Postrhinal cortex (POR)

Retrosplenial cortex

  • Retrosplenial cortex Area 29a (A29a)
  • Retrosplenial cortex Area 29b (A29b)
  • Retrosplenial cortex Area 29ab (A29ab)
  • Retrosplenial cortex Area 29c (A29c)
  • Retrosplenial cortex Area 30 (A30)
Brain regions are three dimensional shapes and displaying these in a 2D visualization requires some visual tricks. Moreover, the origin and termination of connections are not always described in full detail in the anatomical literature. Both these facts make it neccesary to display areas at different levels of spatial detail next to eachother. Area boxes are therefore divided into four quadrants (white dotted lines in Figure 1). In sum:
  • Quadrant I displays full topological information (Figure 1 I).
  • Quadrant II displays information about the septo-tempral/dorso-ventral axis and layers, but not about the proximo-distal/rostro-caudal axis (Figure 1 II).
  • Quadrant III displays information about the proximo-distal/rostro-caudal axis and layers, but not about the septo-tempral/dorso-ventral axis (Figure 1 III).
  • Quadrant IV displays information about the area and layers, without topological information (Figure 1 IV).

Watch the video tutorials on this website - especially video tutorial 2 - to find out how 3D space is represented in the diagram.

In text:
  • 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 (Figure 1B, marked in red) 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.
Now that you are familiar with the four quandrants that make up an area box, you will now be introduced to the visual elements within area boxes. The Subiculum (Sub) area box and A35 will serve as examples.

Figure 3: Top part of the Subiculum area box with proximo-distal axis.

Let us first take a look at the top part of the Subiculum area box (Figure 3). At the very top the word "Sub" is written, which is the abbreviation for Subiculum. In the next row, the words "prox", "int", "dist" and "unsp" are written. These labels specify the proximo-distal axis of the Sub, with "prox" meaning proximal, "int" meaning intermediate and "dist" meaning distal with respect to the DG. The label "unsp" (unspecified) indicates that no information is available on the proximo-distal distribution of these connections. Below the proximo-distal axis three rows of smaller boxes are displayed. These columns of smaller boxes represent the cortical layers that are defined in the Sub at the three levels of the proximo-distal axis or at the unspecified proximo-distal level. The layers in the Sub are the stratum moleculare and the stratum pyramidale. In the Sub the stratum moleculare is subdivided into a superficial (sup) and deep part of the layer.

Figure 4: Subiculum area box with septo-temporal and proximo-distal axis

As explained, a septo-temporal axis is also present in the connectome (Figure 4: grey bar). Therefore, the cortical layers are repeated for the septal (top rows), intermediate (middle rows) and temporal level (bottom rows) of the Sub (Figure 4). This information is once more repeated for the unspecified level of the Sub, in which no septo-temporal subdivision is made (Figure 5):

Figure 5: Unspecified level of the Subiculum area box

Figure 6: The diagram toolbar

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 (see above). The toolbar has 8 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. If the toolbar is closed, clicking the ‘open menu’ button will restore it (Figure 1D, green outline). You can safely ignore the JavaScript warning. It is related to security management of Acrobat PDF. To keep the pdf userfriendly and flexible, we decided to not require an installation of the document on your local system. Therefore Acrobat does not know if the Javascripts in the documents can be trusted and therefore it issues a Warning. In Acrobat X, the search toolbar can also be displayed on the side of the document.
There are two ways of showing connections in the connectome:
  • Use the search menu, from the toolbar.
  • Use the layer navigation pane.

Search Method 1: Search box.

  • Open the search menu by pressing search in the toolbar.
  • Select a brain area from the ‘Area’ listbox (top box in search window). For example, the lateral entorhinal area (LEA).
  • The search and display of the connections can be limited to a particular 3D subregion. For example, in the entorhinal cortex, a dorsolateral-to-ventromedial axis is described. In the 3D axis fields, a selection can be made for the available subdivision of the selected area. In the ‘3D axis 1’, you can select a ‘vertical axis’, e.g. temporal-to-septal, dorsal-to-ventral or dorsolateral-to-ventromedial axis. In the ‘3D axis 2’, you can select the ‘horizontal’ axis, e.g. the proximo-distal axis.
  • The search can also be limited in to include only a particular cortical layer. When you leave the ‘-‘ in the field, connections to / from all layers will be searched for.
  • Select ‘afferent’ of ‘efferent’. If you select ‘efferent, you get the connections that are running from the area selected in the first Area box. If you select ‘afferent’, you get the connections that are running to the area you selected in the first Area box. If you are interested in both the afferent and the efferent connections, you need to perform the search twice.
  • Search results can be filtered to include only a particular area.
  • If you want the add connections to your search, repeat the steps 1-6. If you want to start again, please first clear all connection (‘Clear all’ button in the toolbar).

Search Method 2: Layer Navigation Pane

  • On the left hand side, the layers navigation pane should be visible. If no layers are visible, please check your version of Acrobat Reader (see System Requirements). The layers are alphabetically organized. At the top of the list, a checkbox ‘options’ is available. This layer must be checked, to see the connectome. to select or deselect the figures in the left top corner of the connectome.
  • In order to show or hide connections between areas, you need to use the layers navigation pane on the left side of the screen (Figure 1). By checking a box, you can switch on or off all the projections from a specific sub-area to another (Figure 6). The "eye"-icon appears when the connection is displayed in the diagram area. Layers that are marked with a "lock"-sign are inactive (for instance "areas" in Figure 6) and cannot be selected or excluded ("deselected").

Figure 6: Layer pane - icons

  • By clicking the "+" icon in front for the projection of interest, the list of layer-by-layer connections expands and the "+" icon changes into a "-" icon. Clicking the "-" icon again will collapse all layers again under their main folder.

Figure 7: Layer pane - expanded

  • When the layer-by-layer connections are expanded (Figure 7), a list allows you to individually switch on and off connections. In order for Adobe to draw individual connections, the top checkbox (Figure 8), which in this example is Sub->A35, needs to be selected. This may mean that you need to deselect many individual layers when you wish to view only a specific layer in a "From->To" connection.
  • The reference table on this website provides a way to look up references between two specific areas. In addition, a complete list of all used references with hyperlinks to "PubMed" is provided.

Figure 8: Layer pane - expanded - icons

  • If you deselect the top checkbox, all individual layers underneath the deselected connection will be hidden from the diagram.

The layer names in the layer panel follow a regular syntax which explains what is drawn:

From -> To

Area_axis1_axis2_layer -> Area_axis1_axis2_layer

Area_axis1_layer -> Area_axis1_layer (only for LEA and MEA)

  • Area: abbreviation of the area name
  • Axis 1: septo-temporal axis, dorsolateral-ventromedial or dorso-ventral axis
  • Axis 2: proximo-distal axis or rostro-caudal axis
  • Layer: abbreviation of the cortical layer name

After a search is carried out, the retrieved connections will be drawn in the connectome between the appropriate areas and quadrants. Additionally, an eye-icon will appear in the layers panel on the left (Figure 1E, yellow outline). 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.
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