4. Automated section alignment
Procedure overview
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In this step, select the alignment method and click Perform Section Alignment to align the sections in preparation for 3D
If you aligned the sections in a previous session and are working with the saved case file, you can Use results from previous alignment to skip this step.
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When the section alignment is complete, click Next Step to continue the workflow.
Tools and commands
Automatically align sections
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NeuroInfo identifies the image type as Brightfield or Fluorescence.
If needed, you can correct the image type by clicking the radio button that corresponds to your images.
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Select the method you want to use for alignment:
Method Aligns sections using: Features Accuracy & processing time Rotation
Flipping
Interior image features
Align using shape and image features outline/contour shape and image content 
Highest Align using shape outline/contour shape only
Align using centers centers of the outlines/contours that define each section Lowest Use results from previous alignment: Check the box and click Next Step to skip this step if you've already aligned your sections in a previous session and are working with a case file that includes the alignment results.
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Click Perform Section Alignment.
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A status window will open as the alignment proceeds.
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When complete, a message will display near the bottom of the workflow window, letting you know whether the alignment successfully completed or not.
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About the alignment process
NeuroInfo uses multiple image-registration algorithms.
Image registration identifies a geometric transform that maps points in one image onto corresponding points in another. The registration process adjusts transform parameters to optimize a metric that compares the image intensities at the corresponding points.
The transforms and comparison metrics vary depending on the alignment method you select.