6. Coordinates

-Coordinate systems: Information about the coordinate systems can be found here: https://www.nitrc.org/plugins/mwiki/index.php?title=quicknii:Coordinate_systems

-Image coordinates: Assigning voxel coordinates to image pixels. Find out more here: https://www.nitrc.org/plugins/mwiki/index.php?title=quicknii:Image_coordinates



Voxel coordinates of the mouse cursor can be read from the top-left corner of the main window. Some coordinates for Bregma and Lambda are available for the WHS-SD-Rat atlas, “Coordinates v1 - v1.01.pdf” on https://www.nitrc.org/docman/?group_id=1081 . Using those data, we provide a simple converter page, where voxel-coordinate triplets can be entered and are converted to location related to Bregma and Lambda, expressed in millimeters.

It has to be noted that this is not an exact Stereotactic conversion, distance is measured along the axes of the volume, where Bregma and Lambda have almost a millimeter vertical separation. The volume is tilted forwards approximately by 4 degrees, and it has a small, but noticeable rotation around the vertical axis too.