manual - 3d in the diagram
Connectome user interface
1) After opening the connectome in Acrobat Reader, a view similar to the image below should be visible on your computer screen. 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 in the slide show. (press > to continue)
http://www.temporal-lobe.com/images/temporallobe/Figure_2_600dpi.jpg
In the white outlines here, the hippocampal formation, pre- and parasubiculum are shown.
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.
http://www.temporal-lobe.com/images/temporallobe/white_enclosed_area.png
Area boxes are divided into four quadrants: Example CA1
QI displays full topological information. QII displays information about the septo-tempral/dorso-ventral axis and layers, but not about the proximo-distal/rostro-caudal axis. QIII displays information about the proximo-distal/rostro-caudal axis and layers, but not about the septo-tempral/dorso-ventral axis. QIV displays information about the area and layers, without topological information.
http://www.temporal-lobe.com/images/temporallobe/ca1_quadrants.jpg
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. (You can safely ignore the JavaScript warning)
http://www.temporal-lobe.com/images/temporallobe/toolbar.jpg
Re-open the toolbar.
If the toolbar is closed, clicking the ‘open menu’ button will restore it. In Acrobat X, the search toolbar can also be displayed on the side of the document.
http://www.temporal-lobe.com/images/temporallobe/re-open_toolbar.jpg
search.jpg
Press search on the toolbar to open the search dialog. Select the areas of interest and press OK to execute the search. After a search is carried out, the retrieved connections will be drawn in the diagram between the appropriate areas and quadrants.
example_search_dg-ca3.jpg
This search will retrieve all outgoing connections from the dentate gryrus to CA3.
http://www.temporal-lobe.com/images/temporallobe/example_search_dg-ca3.jpg
Search results.
Displayed are all known anatomical connections running from DG to CA3.
http://www.temporal-lobe.com/images/temporallobe/dg_ca3_search.jpg
Clear all button.
Use the toolbar buttons to clear all lines from the canvas, to start anew. Alternatively, open the search dialog again and start adding connections to the network.
http://www.temporal-lobe.com/images/temporallobe/clear_all.jpg
Figure Panel on interactive connectome.
The connectome pdf has 4 figure panels, which can be accessed using the buttons. The panels provide information about the anatomical regions displayed in the diagram, and the synonims used for these areas in the literature.
http://www.temporal-lobe.com/images/temporallobe/anatomical_background_info.jpg
Use the slideshow on this page to get a quick impression of the rat brain connectome. Use the maximize button on the bottom of the presentation window, to see it full screen. If this connectome is to your liking, you can download it for free. Please create a free user account and login to access the resources related to this project. If you want to have a more detailed introduction about the connectome and what you can learn from it, watch the video.
