Serial Section Assembler workflow >

5. Review alignment

Procedure overview

In this step, you can review and fine-tune the automated section alignment from the previous step to help ensure that the final reconstruction reflects the anatomic structure of the brain as accurately as possible. Fine-tuning the alignment can also correct registration errors, for example, if dorsal surfaces influence registration more than ventral surfaces, serial section alignment can flatten the cortical surface.

1. Set the orientation for the 3D reconstruction.

   When the workflow opens, the first section is displayed. Adjust the rotation so that the section is straight and level; this sets the orientation for the entire volume. For example, many users adjust coronal brain sections so that the midsagittal plane is vertical.

2. Adjust the alignment of each section relative to the previous section in the sequence so that sections are oriented consistently through the reconstruction. To facilitate this process, all sections, apart from the first, are shown superimposed on the previous section.

3. When you complete the process of fine-tuning the alignment of all the sections, click Next Step to continue the workflow.

Tools and commands

Zoom level

• Adjust the Zoom level using the Zoom in and Zoom out buttons so that you can easily see the margins and features of your sections.

• Reset Zoom: resets to the default zoom level

• Alternatively, you can use the Zoom controls on the Move ribbon (some functions are identical) .

Image controls

Many of the image controls are also available as keyboard shortcuts; they are listed at the bottom of the workflow window.

Tools in this section of the workflow window are designed to make it easy for you to:

1. Rotate the first section in the sequence so that it is straight and level. You may want to check the box to Show Grid for this step.

2. Precisely shift subsequent sections to fine-tune the automated section alignment.

Transparency:
	All sections, except the first, are shown superimposed on the previous section—both are semi-transparent by default. Use the transparency slider to control the visibility of both the current and the previous section. As you fine-tune the section alignment using the Shift and Rotate controls, you may find it useful to toggle visibility between the previous and current section.
Shift:
	Use the arrows to move the current section to align it with the previous section. Alternatively you can drag the section with your mouse or shift it with the arrow keys on your keyboard.
Rotate:
	Rotate left or right by the number of degrees in the box just below the button. Use the arrows or type in the box to change the number of degrees the section is rotated when you click the button. Alternatively, you can press comma on your keyboard to rotate left or period to rotate right. Rotate 90° left or right Rotate Volume: Check the box to apply rotation to all of the sections at once from the current section. This may be useful if you weren’t able to determine the tissue orientation from early sections.
Buttons
	Reset: Undo manual adjustments and reset the section position to the result of automatic registration. Flip: Flip or reverse the section along its vertical axis so that features that were on the right are now on the left and vice versa. Refine: Automatically refine the alignment after you have manually adjusted the position of the section (rotation or translation). Metric: Quantitative indication of how well the sections align on a scale of 0 (worst) to 100 (best). This value and its range are relative across brains; you can use it to compare alignment success of sections within an individual brain.

Show grid

Show the grid to assist in orienting sections.

Check the box to superimpose a grid over the display. Use the slider to adjust the cell-size of the grid: slide left for fewer grid lines; slide right for more grid lines.

Moving between sections

Review the alignment of each section that will be used for the reconstruction; use these controls to view each section superimposed on the previous section (except the first section, which is shown alone).

The current section number and the total number of sections is displayed at the top right. Type a section number into the box (center) to display and adjust the alignment of that section. Jump to the first section. Jump to the last section. Move to the previous section. Move to the next section.

Shortcuts

A list of keyboard shortcuts for the Image controls in this workflow step is displayed at the bottom of the window. Using keyboard shortcuts can save considerable time compared to clicking buttons onscreen.

Movement	Hot Key
Move Left	Left arrow
Move Right	Right arrow
Move Up	Up arrow
Move Down	Down arrow
Rotate Left	, (comma)
Rotate Right	. (period)
More Visible	+ (Plus)
Less Visible	- (Minus)
Toggle Visibility	Alt + 0
Rotate Left/Right	Mouse wheel

In this step, the image information shown in the Image Adjustment panel does not reflect the original image data. Instead, it reflects display adjustments used to make the alignment-adjustment process easier to visualize. The original acquired image data is preserved and used for stack reconstruction and output.

 

See 6. Save reconstruction