Setting up planes
To target our dataset, we must setup two different planes: the target plane and the block plane.
The target plane is placed wherever your region of interest is. It will be your final result when you are done cutting with the ultramicrotome.
To place it, click TRACK in the Planes panel:
This will create the target plane at your current position in the BigDataViewer window. This plane will be shown in green in the 3D viewer also:
To adjust the plane, click and drag in the BigDataViewer window to rotate or scroll to translate (this will be updated live in the 3D view also). Once you are happy with your target plane, click TRACK again to stop tracking.
Note scrolling in the BigDataViewer window while tracking is a bit slow - it may be best to find your region of interest with tracking off, then activate it once you're ready.
The block plane marks the surface of your block i.e. the surface you have neatly trimmed with a diamond knife at the ultramicrotome.
You can place it in a similar way to the target plane using TRACK, but it is difficult to accurately align to the block surface manually. Instead, we recommend using a strategy of fitting to points:
To position the block plane, we recommend placing points on the block surface, and fitting a plane to these points. To do this:
- find a view in the BigDataViewer window that provides a cross-section through the block surface.
- right click in the BigDataViewer window and select
Toggle Point Mode. - left click on the surface of the block to create a point. If you add a point by accident, just left click it again to remove it.
- place points at many locations on the surface - try to be as accurate as possible!
- right click in the BigDataViewer window and select
Toggle Point Mode. - right click in the BigDataViewer window and select
Fit To Points.
As you add points, you should see them also appear as spheres in the 3D view:
Once you Fit To Points you should see a blue plane appear in the 3D view. Check this aligns well to your block surface.
To move between planes in the 2D view, click GO TO.
Plane colour C, transparency T and visiblity V can be changed with the corresponding buttons.