Difference between revisions of "BigWarp"

(point to example fiji script on github)
(start updating information for new release 2.0.1)
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| maintainer            = {{Person|Bogovic}}
 
| maintainer            = {{Person|Bogovic}}
 
| source                = {{GitHub|org=saalfeldlab|repo=bigwarp}}
 
| source                = {{GitHub|org=saalfeldlab|repo=bigwarp}}
| latest version        = 1.0.0
+
| latest version        = 2.0.1
 
| status                = stable
 
| status                = stable
 
| category              = [[:Category:Plugins|Plugins]], [[:Category:Visualization|Visualization]], [[:Category:Transform|Transform]]
 
| category              = [[:Category:Plugins|Plugins]], [[:Category:Visualization|Visualization]], [[:Category:Transform|Transform]]
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The following table shows the available landmark placement commands and keystrokes.  
 
The following table shows the available landmark placement commands and keystrokes.  
 
{| border="1" style="border-collapse:collapse;"
 
{| border="1" style="border-collapse:collapse;"
| style="padding: 5px;" | {{key press|Spacebar}}
+
| style="padding: 5px;" | {{key hold|Spacebar}}
 
| style="padding: 5px;" | Toggle ''Landmark mode''  
 
| style="padding: 5px;" | Toggle ''Landmark mode''  
 
|-
 
|-
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|}
 
|}
  
=== Navigation ===
+
=== Navigation and Visualization ===
  
 
Bigwarp shares many navigation features with BigDataViewer, the details of which can be
 
Bigwarp shares many navigation features with BigDataViewer, the details of which can be
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|-
 
|-
 
| style="padding: 5px;" | {{key press|R}}
 
| style="padding: 5px;" | {{key press|R}}
| style="padding: 5px;" | Resets the active viewer.  
+
| style="padding: 5px;" | Resets the active viewer.
 +
|-
 +
| style="padding: 5px;" | {{key press|U}}
 +
| style="padding: 5px;" | Show warp visualization / grid dialog.
 +
|-
 +
| style="padding: 5px;" | {{key press|F6}}
 +
| style="padding: 5px;" | Show moving image panel Visibility & and Grouping dialog.
 +
|-
 +
| style="padding: 5px;" | {{key press|F7}}
 +
| style="padding: 5px;" | Show target image panel Visibility & and Grouping dialog.
 
|}
 
|}

Revision as of 10:48, 21 December 2015

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

Landmark placements is done in Landmark mode which can be toggled with Spacebar. Users place pairs of corresponding points on

The following table shows the available landmark placement commands and keystrokes.

Template:Key hold 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.

Navigation and Visualization

Bigwarp shares many navigation features with BigDataViewer, the details of which can be found on the BigDataViewer Navigation 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.