AligNII

AligNII is a tool for anchoring 2D histological sections to a 3D template volume set.
The basic functionality provided is viewing arbitrary rectangular slices from the volumes. The rectangular slice can be freely manipulated in terms of setting its position, its orientation and its size.

Navigation using standard planes video

The three standard planes on the right let you drag and rotate the slice. Drag the red midpoint (becomes yellow when the mouse cursor is over it) to move the slice. Drag anywhere else to rotate the slice.

Panning the main slice video

The main view supports moving of the slice in its own plane. Drag anywhere to move the slice.

Stepwise navigation video

Stepwise movement and rotation controls are provided for each slice window. Movement step is set in voxels, rotation step is set in degrees. This is the only way to rotate the slice in its own plane.

Dataset and contrast video

Image modalities can be switched any time. For images with continuous values, contrast range and gray/colorscale selection controls are provided.

Move the mouse cursor over the image to highlight active areas. Highlights link to related videos. Move the mouse cursor away from the image to see the original user interface.

The advanced functionality adds an overlaid histological section and supports visual anchoring of the section into 3D space.

Using the image overlay video

Top (H) and bottom (V) toggle buttons switch between the histological image (H) or the MRI slice (V). The slider on the left adjusts custom blending of the histological image and the MRI slice. Pushing the toggle button again switches back to blended image.

Stepwise resizing video

Stepwise controls are provided for setting width and height of the slice. Decreasing width and height zooms in, increasing width and height results in zooming out.

Visual stretching video

  1. Set a fixed point by pressing the SPACE bar. A green cross marks the fixed point.
  2. Select horizontal or vertical stretching mode using the new buttons in the window header. Arrowheads indicate the active streching mode.
  3. Drag anywhere on the slice to stretch. Live preview of the stretching operation is provided.
Press Esc, Delete or Backspace to remove the fixed point. For smooth control, keep some distance between the fixed point and the point to be dragged. The tool switches back to panning mode after each stretching operation.

Move the mouse cursor over the image to highlight active areas. Highlights link to related videos. Move the mouse cursor away from the image to see the original user interface.

Supported by the European Commission FP7 (The Human Brain Project) and Uninett Sigma.