BigWarp
| BigWarp (Fiji) | |
|---|---|
| Author | John Bogovic |
| Maintainer | John Bogovic |
| Source | on GitHub |
| Latest version | 2.0.1 |
| Development status | stable |
| Category | Plugins, Visualization, Transform |
Contents
Description
Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.
The interface enables landmark pair placement and displays the effects of the warp on-the-fly.
Installation
Bigwarp comes with Fiji. You can access it via Plugins › BigDataViewer › Big Warp, or by modifying this example script.
Usage
Open two images in ImageJ, one moving and the other target and navigate to Plugins › BigDataViewer › Big Warp. A dialog will appear prompting selection of the moving and target images.
Getting Help
Press F1 at any time to open a help page with a listing of navigation and editing commands.
Landmark point placement
Landmark placements is done in Landmark mode which you enter by holding Spacebar. Users place pairs of corresponding points on
The following table shows the available landmark placement commands and keystrokes.
| hold Spacebar | Toggle Landmark mode |
| <Landmark mode on>+left-click | Clicking while in landmark mode adds a landmark point. |
| <Landmark mode on>+left-click+drag | Clicking an existing point and dragging changes it's position. |
| <Landmark mode on>+⇧ Shift+left-click+drag | "Move" a point. The initial click places a
landmark point for the moving image. The release places a landmark point for the target image. |
Bigwarp inherits many image navigation, visualization, and grouping features with BigDataViewer, the details of which can be found on the BigDataViewer page or on the help page. BigWarp specific features are documented below.
The following table shows the available navigation commands using the mouse:
| Q | Align the non-active viewer with the active viewer. |
| W | Align the active viewer with the non-active viewer. |
| R | Resets the active viewer. |
| U | Show warp visualization / grid dialog. |
| F6 | Show moving image panel Visibility & and Grouping dialog. |
| F7 | Show target image panel Visibility & and Grouping dialog. |
