Assigning Vertices

Once our planes our set, we have to mark the vertices of our block face. These are the four corners of our nicely trimmed surface.

Placing the vertices

1. Click GOTO in the planes panel, to move the 2D view to your block plane. You should see your trimmed surface.
2. Right click in the BigDataViewer window and select Toggle Vertex Mode
3. Click on the four corners of your block face - try to be as accurate as possible!
4. Right click in the BigDataViewer window and select Toggle Vertex Mode

The vertices should now be marked by blue points:

Assigning vertices

For the calculation to work properly, you must now decide on the orientation your block will have in the microtome holder i.e. which side of your block will face up? Choose something you can easily find back at the microtome later e.g. I often choose the top side of the block to be the one the sample has sunk down against during embedding.

To tell the software your chosen orientation, you must assign the vertices as either: Top Left, Top Right, Bottom Left or Bottom Right. Do this by clicking on a vertex (it should highlight in red), and then clicking the corresponding button in the Assign Vertex panel:

Text will show you your assignments in the 2D view and 3D view. In the 3D view they are abbreviated to two letters e.g. Top Left = TL. It is important to check your assignments make sense on the 3D view! The 2D view can be misleading, as you do not know which direction you are viewing the block face from e.g. from 'inside' the block, or from 'outside' the block.

A finished assignment will look like below: