JIV2 demo:

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The java applet (JIV2) should show four columns of data. The first shows a sample Cynomolgus macaque in its native space. The second contains the MNI macaque stereotaxic model. It was created by non-linearly registering and average MRI data from 25 rhesus & cynomolgus macaques (see here for more information ). The rightmost column contains labels from the CoCoMac application. These labels come orginally from the Paxinos Atlas and were nonlinearly warped to fit on the MNI MRI rhesus steretaxic model. The third column contains a blend of the second and rightmost columns which is controlled by the slider at the base of the column.

The MNI MRI macaque stereotaxic coordinates (X,Y,Z) are displayed in the first row below the volumes. The second row displays the native volume's coordinates (Xnat,Ynat,Znat), and the third row displays the paxinos atlas coordinates (Breg,Lat,Sup). 'Breg' is the Bregman #, 'Lat' is the medial to lateral distance on the figure, and 'Sup' is the inferior/superior distance - measured using the ruler on the left side. The fourth row shows the atlas label corresponding to the cursor's position (Anatomy), and the intensity of the volume (I).

One can use the left most mouse button to click on any image, in any column, and the other three images will be updated with the appropriate position (and across the columns too, if sync mode is on). You can also hold the middle/rocker mouse button down while moving up or down, to pan through the image plane. Holding 'Shift' with the left or middle mouse button will allow zooming and re-centering of the volume.

In the JIV2 window, you can "right-click" to get popup menus. One useful aspect is to turn on the 'sync all cursors' option so that all three column are updated with each left mouse click.

When looking at the images, remember that left is left and right is right!

For information or to download JIV2, the Java Image Viewer v2.0, please see here.

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