Registration windows and tools reference

Context

Learn about the tools and software layout for registering brain images to reference-brain atlases

When you click Register Sections or Register Volume on the Registration ribbon, tools for aligning your image(s) with a reference-brain atlas are displayed. You'll see the following: The main viewing window changes to a four-panel display designed to make the registration process clear and intuitive. The 3D Slice Scroll tool is available for moving the slice view. Tools that facilitate the registration process are displayed on the Registration ribbon. Other tools will be displayed on the Registration ribbon once you click leave registration.

See instructions for Register sections and Register volume.

Main viewing window

In Registration mode, the main NeuroInfo viewing window is a set of four panels:

• 3D views on the left: On the left side are 3D visualizations of the experimental image (top) and the reference-brain atlas (bottom); both are maximum intensity projections.

  • The thin red rectangle in each view indicates the current plane that is displayed in the corresponding right-hand panel.

  • The yellow ball represents your cursor location

• Slice views on the right: The images on the right side display the section or optical section indicated by the thin red rectangle in the 3D visualizations on the left:

  • The current plane (or slice) of the experimental image is in the top-right.

  • The atlas brain is displayed bottom-right. Before registration, only the center plane of the reference brain is displayed; once you have registered one or more sections, the current plane of the reference brain is displayed.

• Specimen orientation: Letters in each of the four panels provide orientation information. You will see the following depending on the view orientation:

  • D and V: dorsal and ventral

  • R and C: rostral and caudal

  • L and R: left and right

Navigating images

• The location of your cursor is represented as a yellow ball in all four viewing panels.

• Hover your mouse on a panel to make it active; the panel label (e.g., experiment slice for the top right panel) is highlighted in bright green to indicate that the panel is active.

• Move the slice display using the 3D Slice Scroll tool located on the right side of the NeuroInfo window. Note that you can move the tool if desired; it is a dockable window.

• Alternatively, you can move the slice display using the Orthoview tool. Open it from the Workspace ribbon.

• Zoom in or out in the active panel by scrolling your mouse wheel.

• Change the orientation of the 3D visualizations (experimental and atlas) or return to the original orientation using the buttons in the registration ribbon:

Registration panel overview

The Register sections to atlas and Register volume to atlas panels (dockable windows) include three tabs, each containing a different group of related registration tools (see image on the right). Click the tab to view its contents.

Registration

Tools to select the reference-brain atlas that you want to use and to register (align) your brain images to the reference atlas are organized in sections accessed by clicking the dropdown indicators.

Atlas Ontology

Atlas ontology tools to view and display all of the anatomic structures and regions that are defined in the brain atlas chosen for the registration. You can also create and edit groups of structures and regions that are pertinent for your research.

Visualization

Visualization controls for the 3-dimensional display of experimental images and any modeled structures.

Registration ribbon—in registration mode

When you click Register Sections or Register Volume, you enter registration mode, and the Registration ribbon at the top of the screen changes to display tools specific for brain-atlas registration. Functions of the tools are described below:

Transform Files
	Registration Transforms: Use the drop-down menu to access tools for loading and saving "Transforms". Note that saving your data file from within the registration tool saves the transform or transform set so that it will be reloaded when you re-open the data file. Transform: maps geometric points from one physical coordinate space into another. In NeuroInfo, transforms essentially alter the size, shape, and/or sectioning angle of the reference atlas to match those features of the experimental section. Transform Set: a collection of transforms, one for each section in a serial section registration. Transform Sets are not relevant for image-volume registration. When registering multiple sections, save sets of transforms in separate folders to avoid overwriting or mixing results from different animals or registration attempts. Clear All Transforms: Clear or "unload" any transforms or transform sets from the current data file.
Orientation
	Reset: Return to the original image orientation.
	Coronal: View coronal orientation.
	Sagittal: View the sagittal orientation.
	Transverse: View the transverse orientation.
Mapping
	Hide Tracing: Hide tracing data, such as markers and contours.
	Select Anatomy: When enabled, click in the Experiment- or Atlas-Slice views to select and view the structure that is defined in the brain atlas at the location.
	Deselect Anatomy: Click to deselect and stop viewing brain structures defined in the atlas.
	Map Experiment to Atlas: Map experimental data (markers and 2D contours) into the common reference space of the brain atlas used for the registration.
	Map Atlas to Experiment: Map selected brain anatomic regions from the atlas onto the experiment.
	Analysis: Displays quantitative information about the brain regions identified in your images.
Exit
	Leave Registration: Exit registration mode; the buttons on the ribbon will change back to tools that are not part of the image registration process and the Register to Atlas panel of tools on the right closes.