ImageJ

BigWarp plugin for Fiji
Project	Fiji
URL	https://imagej.net/BigWarp
Source	on GitHub
License	GPLv2
Release	3.0.0
Date	Thu May 25 12:57:29 CDT 2017
Development status	Active
Support status	Active
Team
Founders	John Bogovic, Stephan Saalfeld
Leads	John Bogovic, Stephan Saalfeld
Developers	John Bogovic, Stephan Saalfeld
Debuggers	John Bogovic, Stephan Saalfeld
Reviewers	John Bogovic, Stephan Saalfeld
Support	John Bogovic, Stephan Saalfeld
Maintainers	John Bogovic, Stephan Saalfeld
Contributors	Curtis Rueden, Mark Hiner

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. If this is not visible in your installation, try updating Fiji with Help › Update Fiji.

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 in the viewer

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 commands and keystrokes for landmark placement, warping.

T	Toggle between warped view and raw view or moving image.
^ Ctrl+O	Open landmarks from saved file.
^ Ctrl+S	Save current landmarks to a file.
hold Spacebar	Toggle Landmark mode
<Landmark mode>+left-click	Clicking while in landmark mode adds a landmark point or selects and existing landmark.
<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.
^ Ctrl + Z	Undo the last landmark point change.
^ Ctrl + Y	Redo the last landmark point change.
V	Toggle point visibility in the viewer.
N	Toggle point name visibility in the viewer.

Landmark selection and editing in the table

Some changes to landmarks can be done by interacting with the landmark table.

left-click	Select row.
^ Ctrl+left-click	Add row to selection.
⇧ Shift+left-click	Select range of rows.
⎋ Esc	Deselect all rows.
<Landmark mode>+left-click	Removes one landmark.
right-click › Delete	Deletes a landmark pair (row in the table).
right-click › Delete all selected	Deletes all selected landmark pairs (row in the table).

Notes on point addition and landmark pair selection

• Adding a new landmark pair selects that pair (row) in the table.
• If a row is "missing" a moving (target) landmark point, then it must be selected in order to add that missing point by clicking in the moving (target) viewer. Then BigWarp will find the "next" row that is missing a moving (target) landmark, and select that row automatically.
• If the selected row is not missing a landmark, the next click will add a new landmark pair.
• If multiple rows are selected when a viewer is clicked, the result will be as though only the first row was selected.

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.
E	Centers the active viewer to the nearest landmark (considers 3D when applicable).
^ Ctrl+D	Centers the active viewer to the next landmark.
^ Ctrl+⇧ Shift+D	Centers the active viewer to the previous landmark.
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.
^ Ctrl+E	Export moving image as an ImagePlus.
^ Ctrl+⇧ Shift+E	Export moving image as a Virtual ImagePlus.

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. )

The warped moving image can be exported as an in-memory or virtual ImagePlus. A virtual ImagePlus is generally faster to generate but slower to browse, whereas an in-memory ImagePlus will be slower to generate but faster to browse.

The exported image will have the same dimensions as the target image. Note: Take care when exporting very large data sets.