The alignment tab is visible as soon as you enter the alignment mode. For more information, see Activating the Alignment Process.

You can perform Three-Point Alignment:

  • Line-up an imported image with reference marks, such as the precision fiducials on a CorrMic Holder.
  • Line-up features in an imported image with LM, EM and SEM images of the same features.
  • Line-up a session of LM, EM and SEM imagery with previously acquired LM, EM and SEM imagery session.

With the three-point alignment process you can set the position, rotation, and scale of an image or tile. This is used to line the image or tile up with reference marks or other images. Once an image is lined up, it can be used as a reference (road map) to move the stage to control further image acquisition.

Parameter

Description

Alignment Mode

Sets which data properties you can change during the alignment.

-

Translate Only

Moves the item you are aligning in x and y only without changing its size or orientation.

-

Translate and Rotate Only

Moves the item in x and y direction and changes its orientation. It does not change the scale of the item you are aligning.

-

Translate, Rotate and Scale Only

Moves, reorients, and resizes the item you are aligning. It does not shear it.

-

Translate, Rotate, Scale and Shear

Supports full three-point alignment.

-

Alignment Handles

Displays alignment handles to rotate and resize the image.

-

3D Alignment

Displays options to align an image in z direction and for three dimensional rotation.


Flip Horizontally

Mirrors the image horizontally.


Flip Vertically

Mirrors the image vertically.


Flip in Z

Mirrors the image stack in z direction around the middle z-height.

Relative Z Offset

Only visible if 3D Alignment is selected.
Sets the z offset for the selected image.

Step Size

Only visible if 3D Alignment is selected.
Sets the step size for the Relative Z Offset input.

Set to current Global-Z

Only visible, if 3D Alignment is selected and only active if the Global-Z slider is activated on the Dimensions tab.
Sets the z value of the currently selected Global-Z as the z value for the center of the z-stack.

Apply 3D Rotation

Only visible, if 3D Alignment is selected.
Enables the controls below for the three dimensional rotation of the z-stack.

-

Rotation X-Axis

Sets the rotation along the x-axis with the slider or input field. Click on the button to reset the angle.

-

Rotation Y-Axis

Sets the rotation along the y-axis with the slider or input field. Click on the button to reset the angle.

-

Rotation Z-Axis

Sets the rotation along the z-axis with the slider or input field. Click on the button to reset the angle.

-

Angle Step Size

Sets the angle step size for the slider/input fields above.

-

View Cube Control

With this cube control, you can rotate the stack interactively. It has a visual representation of the current stack (white box) and the cutting plane which is displayed in the 2D view above.

-

Presets

Sets the View Cube Control to a predefined position. You can set it to the Default, or you can select an orientation from the dropdown of the button to show the Default, Viewer Perspective, Left, or Right orientation.

-

Manual Control

Controls the orientation of the View Cube Control.

Reset

Resets the alignment as it was when you started this alignment operation.

Clear

Resets the alignment to where it was when the data was first acquired or imported.

Finish

Exits from the alignment operation, keeping the alignment you have established.

Cancel

Returns to the alignment as it was when you started, and exits from the alignment operation.