BigWarp

Revision as of 16:32, 21 December 2015 by Bogovic (talk | contribs) (doc ctrl-click for point pin)
BigWarp (Fiji)
Author John Bogovic
Maintainer John Bogovic
Source on GitHub
Latest version 2.0.1
Development status stable
Category Plugins, Visualization, Transform


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 and display

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>+left-click Clicking while in landmark mode adds a landmark point.
<Landmark mode>+left-click+drag Clicking an existing point and dragging changes it's position.
<Landmark mode>+ 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.

<Landmark mode>+^ Ctrl+left-click "Pin" a point. Add a landmark at the same location for both moving and target images.
V Toggle point visibility in the viewer.
N Toggle point name visibility in the viewer.

Navigation and Visualization

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.

Import and Export

Landmarks can be exported and imported from plain text files using the drop down menu in the landmark table panel ( File › Export (Import) landmarks. )

Bigwarp export.png

The warped moving image can be exported as an in-memory or virtual ImagePlus. Note: This may not be a good idea when the target image is very large.