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

Default Full View

In Registration mode, the default view in the main NeuroInfo window shows a set of four panels:

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

    • The thin red rectangle in each 3D view indicates the current plane that is displayed in the corresponding right-hand panel.

    • The yellow ball represents the cursor location in either Slice view that are in the right panels

  • 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, labeled Experiment Slice.

    • The atlas brain is displayed bottom-right, labeled Atlas Slice. 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

Experimental Slice View

Click Experimental Slice View to display only the Experiment Slice view in the main NeuroInfo window. This corresponds to the top right image in the Default Full View.

  • Experimental Slice View enlarges the experimental slice view that displays the current section or optical section.

  • This view is helpful for seeing details in the image.

  • Adjust the visibility of the atlas overlay and other settings using the visualization options controls .

  • Click Default Full View to return to the view showing all four panels as described above.

Navigating images

  • The location of the cursor in either Slice panel (i.e., Experiment Slice or Atlas Slice) is represented as a yellow ball in the 3D panels on the left.

  • Hover the 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 Orientation 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; click the drop-down indicators to expand each section. The specific

Current Calibration: Create, Edit, or Activate the calibration that specifies the reference-brain atlas you're using for the registration, specimen orientation and scaling information.

Once you have activated the calibration for your registration, you may want to collapse this section.

Registration: Tools and controls for automatically registering (aligning) your brain images to a reference brain atlas. The tools displayed depend on whether you want to register sections or register a volume.

Registration Info: Enter image information and view quantitative registration information.

Image Info:

  • Modality: Verify or change the microscopy mode for the experimental specimen.

  • Channel: Verify or change the color channel that contains the cytoarchitectural information needed for the registration process.

Registration Info: Diagnostic information about your registration (alignment).

Visualization Options: Controls for viewing and hiding the atlas overlay in the Experimental slice view, anatomic regions defined in the atlas, and tracing data in image files.

  • Show atlas over experiment slice: Toggle display of the current atlas slice superimposed on the experiment slice on and off (top-right pane of the main NeuroInfo window)

    Transparency: Adjust the transparency of the atlas image.

  • Show anatomic regions: Toggle display of selected anatomic regions on and off. When checked, anatomic regions are displayed in the two bottom panels that represent the atlas and in the experiment slice pane (top-right).

    Transparency: Adjust the transparency of anatomic regions

  • Show Slice Indicator in the Atlas and Experimental View: In the 3D views on the left (Experiment and Atlas), toggle display of the red line that indicates the current slice shown in slice-view panels on the right (Experiment Slice and Atlas Slice).

    This may be of interest for creating figures to share your results.

  • Clip Tracings: Restrict display of markers and contours to the current experiment slice. If you have markers for automatically detected cells, we recommend that you check the box to Clip Tracings.

    Click Hide Tracings in the Registration ribbon to toggle the display of all markers and contours on and off.

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: A transform maps geometric points from one physical coordinate space into another. NeuroInfo creates one or more transforms as the result of registering a brain image or series of brain-section images to a brain atlas. Transforms record the alterations in the size, shape, and/or sectioning angle of the reference atlas needed to register (align) the experimental brain image to the atlas.

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.

Display

Experimental Slice View: Display only the Experiment Slice view in the main NeuroInfo window

Default Full View: A set of four image panels, with3D visualizations on the left side and slice views on the right. The top two images are the experimental sample and the bottom panel are the selected brain atlas

Hide Tracing: Hide tracing data, such as markers and contours.

Mapping

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: Display 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.