You can show opaque three dimensional structures of the brain by "showing" or "hiding" structures from this menu. The "Transparent" function allows you to see transparent views of the structures to view the anatomical relationships between them.
Selecting the sagittal, coronal or horizontal sections (or clicking on one of the section image buttons in the toolbar) will superimpose a single plane of the MRI images from each brain on your image space. These planes can be moved once the selection tool mode button in the toolbar is selected. Selecting "Show Annotation on Section" from this menu will color the MRI images according to the brain structure ontology.
When you have a gene selected, the Gene Tab menu allows to you to show all expression, hide all expression (for instance to then select a single structure) or toggle expression (for instance, unselect your region of interest then toggle to see expression in only that region).
You can also show or remove threshold controls and choose the visual representation of your data (raw data vs. z-score) from this menu.
To be taken to the gene detail page, select "Get Info". To see the Multiplanar view, choose "View Images". These functions are also available by right-clicking on the gene name in the Gene List.
When this function is selected, either by toggling the cutting tools button in the toolbar or selecting "Clipping Planes" from the View drop down menu, you can make coronal, sagittal or horizontal cuts in your view of the brain and related data. To cut in a particular plane, make sure the cursor is in selection tool mode, and then click and drag on the plane you are interested in clipping.
Image and Probe Navigation
In the image at left you see the 2D images associated with the point selected by the MRI crosshairs. The viewer on the left hand shows a larger view of the brain specimen, with a blue highlight around the chunk of that specimen from which the current sample was taken. The viewer on the right hand shows a detailed view of that chunk, with structure annotations visible.
You can navigate from the image viewers as well. The strip of thumbnail images at the bottom of each viewer shows all of the images from its parent specimen, in sectioning order. Clicking on a thumbnail image in the left hand viewer will move the MRI crosshairs and open a new set of images in the right hand viewer. Click on one of the structures to move the MRI crosshairs to the location where that structure was sampled. As you move your mouse over the structures in the right hand viewer its name will appear in the upper-left corner of the viewer.
Use the toolbar icons to add or remove structure annotations such as structure outline, structure colors, and structure labels. To show all specimen images from this block in order, including the Nissl, ISH, SMI-32 and pre- and post-cut LCM images, click . To see the block face images, click . Use the full-page viewer icon to launch a new full-page viewer in a new window for the current image set.