Workflow step 5: Align the sections
In this step, NeuroInfo automatically aligns the sections previously delineated with the contours. During the alignment process, NeuroInfo has the ability to correct for flipped or damaged sections. You can review and correct the alignment in the next step.
- NeuroInfo automatically identifies the image type as Brightfield or Fluorescent.
- Select one of the three methods (described below in the table).
- Click the Perform Section Alignment button.
If the type is Brightfield but you only need to use one color, select Fluorescent then select a channel for alignment from the drop-down menu.
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.