Atlas of the HUMAN BRAIN
Atlas of the HUMAN BRAIN

Navigator Help


If the applet does't run ...

The online version of the Brain Navigator is a Java applet, a small program capable to run inside your Web browser window. To make this possible you must have installed the Java runtime (1.4x or newer) on your computer. If you don't have already done so please install Java on your computer (available free of charge for several platforms from Sun ( We tested the Navigator applet with Linux and several Windows versions using Firefox, Opera and Internet Explorer. It should also run on MacOs X (with Java 1.4) but we didn't test this. For telling us your experiences or problems with the Navigator applet please use our contact form.
Please also check your browser preferences and make sure to allow Java inside a Web page!


Normal appearance of the Navigator applet

loading applet ...If everything is correctly installed the Navigator applet should load (indicated by a moving bar) and - after some time (dependent on your internet connection speed) -
finally start up with two windows looking like the following:

Navigator applet (normal view)

One is a popup window and can be moved around with the mouse. It shows a colorful schematic frontal brain slice and the names of structures under the mouse pointer. The popup window  may be hidden behind your main browser window. You can bring it on top or hide it with a button. Please place it somewhere on your screen, where it doesn't overlap with other windows. The big window is used for navigation through the brain. It shows a coronal, a horizontal and a sagittal cut  through the brain. The point of interest is indicated by a crosshair. Click anywhere inside one of the views to change the position. Note that the image displayed in the popup window changes synchronously (it always shows the right hemisphere of the actual coronal slice). Sequentially moving through a series of slices is also possible. Press the button indicating  your desired orientation (C=coronal, H=horizontal, S=sagittal) and move the slider with the mouse or click on the arrows.
Zero brings you back to the anterior commissure (the origin of the coordinate system). For more about coordinates please read the following chapter.

Some features like ShowHistology and SubCx (=Subcortex) are only available in the full version of the Navigator (coming with the printed Atlas of the Human Brain, 2nd ed. - if you own this book please don't use the program from CD, download your free update from instead.)
The Navigator applet only demonstrates these features and displays some information.
The switch (photo | plate) allows to view the original stained slice (photo) instead of of the colored schema (plate) in the popup window and vice versa. Note that unlike the full version the applet only includes few photos.


Why coordinates and how to enter them

Every point in the atlas space is a  3d coordinate. You can use this coordinate to directly jump to a specific place in the brain or to lookup or reference a structure at a given position.
The Navigator uses two coordinate systems: The Atlas of the Human Brain system and  the Talairach system. Both have the same origin but differ in detail. It is possible to switch between these two systems and to enter coordinates directly. For this the following multipurpose panel is used:
The x, y and z fields tell you the position of the crosshair in mm using the coordinate system indicated below (here: Atlas of the Human Brain). Please click on the Change button to switch to Talairach system and back. If you are moving your mouse above the popup window don't be surprised because the values of  the fields change to show the actual position of the mouse pointer. If the mouse leaves the popup window the original values are restored. 
To directly enter coordinates click on the x, y or z-field and type in a new position. (Use the English numeric notation, don't use a comma). Press the Enter key or click on a different field to complete. The crosshair now moves to the new position and different brainslices are shown. Note: Because The resolution of the Navigator is limited the coordinates you entered may be changed slightly to a nearby value.

Sometimes the entry of more than one point is necessary, e.g. if data from literature shall be compared with own findings. For this purpose a special entry form ( can be used together with the Navigator applet. (Please make sure to allow JavaScript in your browser preferences before using this form!)

First choose your coordinate system (Talairach or Atlas of the Human Brain) Then type in your x, y and z-coordinates into the respective fields. You may choose a label for every point. Click on 'Add Coordinate' to add your data to the list. Continue with additional points or click on 'Import into Navigator' . The Navigator then takes your data and shows every point as a small circle. The crosshair will be placed on your first datapoint. If you place the mouse cursor on one of the circles in the popup window your label will be displayed at the bottom.
Try the button 'Import Demo Coordinates. A big number of circles appear derived from several functional MRI studies. The red circles belong to the right hemisphere, the green circles to the left. This color code has been necessary, because in the popup window only the right hemisphere is shown. In this window the data from the left hemisphere is mirrored and shown in green. If you click on one of these circles the crosshair is adjusted to the center of the circle in all 3 views. (If you click on a circle from the demo dataset additional information about the referenced study is displayed in a separate window).