Microtome Mode
Once all the planes and points are setup, we are ready to go to the microtome.
Now, you will align to your block face, ensuring the bottom edge of your block is aligned to the knife edge. Make sure you are using the same orientation you specified in the plugin!
Make a note of the knife angle and the tilt angle of the arc (in degrees). These must be entered into the Microtome Setup panel:
Once the setup values are entered, you can click Enter Microtome Mode in the Microtome Controls panel.
This will create a basic 3D model of a microtome in the 3D view, showing the knife and arc components, and placing your image in the correct orientation.
This virtual microtome can be controlled with the sliders in the microtome controls panel.
The final slider of this panel is the most important - Solution Rotation.
Each solution (i.e. the combination of angles and distances to reach your target) is tied to a specific rotation angle. There are many possible solutions! Move the slider to view the different options.
The current settings are listed in the Current Settings panel. These are:
- Knife - the current knife angle (degrees)
- Tilt - the current tilt angle of the arc (degrees)
- Rotation - the current rotation angle of the holder (degrees)
- Knife-Target Angle - the current angle between the knife and the target plane (degrees)
- First Touch - the first vertex that will be touched, given the current solution
- Distance to cut - the distance to cut to reach your target, given the current solution. Note - the units here, are the same as used to define the pixel size of your image (e.g. if you set your pixel size to 0.5x0.5x0.5 micron, then the distance will be in microns).
Note - due to the constraints of microtome movement, not every angle will have a valid solution. A valid solution will cause the target plane to turn red, and will show a First Touch and Distance to cut in the Current Settings panel. Invalid solutions will have a green target plane, with no listed First Touch or Distance to cut. If there are no solutions at any rotation angle, you will have to revise your target plane! Some targets are not possible given the constraints of the microtome e.g. a target plane at 90 degrees to the block face will always be impossible to target.