Module: FIB Stack Wizard ()

Description:

This module performs operations for FIB/SEM data set processing:

• Step 1 - Crop before alignment
  Optional operation for cropping the data set.
  Adjust the cropping box and click on the OK button of the dialog.
  Click directly on "Skip" if no cropping is required.
• Step 2 - Alignment
  Alignment using least squares method or gravity centers.
  Click on "Skip" if no alignment is required.
  Set the desired method and click on the Apply button. Rotations are disabled by default. The alignment is performed. When finished, a dialog box prompts the user so save the transformation matrices. Click on "Don't Save" unless you wish to save the transformation applied to each slice in the parameters of the input data set. See Align Slices
• Step 3 - Crop after alignment
  Optional operation for cropping the data set.
  It can be useful, in some cases, to crop the data set after the alignment process in order to keep only the area of interest. Adjust the cropping box and click on the Ok button of the dialog.
  Click directly on "Skip" if no cropping is required.
• Step 4 - Shearing correction
  Optional operation consisting of xy-slice shifting in the y direction.
  The shift is proportional to the z-coordinate of the slice, resulting in a shear-operation. The angle between the original and the sheared z-axis can be specified in the port shear angle.
  Click on "Skip" if no shearing correction is required. See Shear
• Step 4 - Shading correction
  This operation consists of correcting the shading from a pre-computed background with an histogram spreading pixel by pixel. You'll first have to define the region for background computation with a threshold. The selected background should be as uniform as possible, and should not include saturated areas. In some cases, where the chosen background is not uniform, strange artifacts may appear due to internal polynomial computations used to correct the shading. Adjust the mask with the threshold sliders. Select all (the default) if no mask is required.
  Then click on the Skip button to perform shading correction.

Note: The viewer camera is set to orthographic mode when module is created and reset to original mode when the module is removed. You can change the camera mode at any time by using the viewer toolbar button for camera mode.

Connections:

Data [required]
Image data to be processed.

Mask [optional]
Label image data defining the computation area of the alignment.

Ports:

Slice Number

This port controls the slice number of the Ortho Slice connected to the input data.

Slice Orientation

This port controls the orientation of the Ortho Slice connected to the input data.

Wizard Controls

Info

This port displays information about the current action.

Action

This port contains the 3 buttons "Back", "Skip" and "Apply" triggering the actions to perform.

Align Method

[Step 2] This port defines the method used for the alignment (gravity centers or least-squares). See Align Slices

Enable Rotation

[Step 2] This port enables the rotation between two consecutive slices during the alignment computation. False by default.

Shear Angle

[Step 4] This port defines the angle to use when performing the shearing operation.

Low Mask Threshold

[Step 5] This port controls the value range of the internal mask threshold, when a region must be used as a mask for the background computation.

Shading Correction

[Step 5] This port controls the shading correction parameter.