|BigWarp plugin for Fiji|
|Date||Thu May 25 12:57:29 CDT 2017|
|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.
- 1 Installation
- 2 Usage
- 2.1 Getting Help
- 2.2 Landmark point placement and display in the viewer
- 2.3 Landmark selection and editing in the table
- 2.4 Notes on point addition and landmark pair selection
- 2.5 Navigation and Visualization
- 2.6 Commands shared with BigDataViewer
- 2.7 Import and Export
- 2.8 Apply transforms
- 3 Tutorials
- 4 Publication
- 5 Publications using BigWarp
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.
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.
Once the two image windows and one table window open, click on a point in the moving image, then click on the corresponding point in the target image. After you have a few moving-target point pairs, press T to transform the moving image (you may need to re-navigate if the two image are very far apart: see the Q and W hotkeys below).
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 moving and target images.
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.
|^ 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.
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
|^ Ctrl+E||Export moving image as an ImagePlus.|
|^ Ctrl+⇧ Shift+E||Export moving image as a Virtual ImagePlus.|
- Displaying multiple stacks ("sources")
- Grouping sources
- Adjusting brightness and color
- Bookmarking views (locations and orientations)
|left-click+drag||Rotate (pan and tilt) around the point where the mouse was clicked.|
|right-click+drag or middle-click+drag||Translate in the XY-plane.|
|mouse-wheel||Move along the z-axis.|
|⌘ Cmd+mouse-wheel or ⇧ Shift+^ Ctrl+mouse-wheel||Zoom in and out.|
|X, Y, Z||Select keyboard rotation axis.|
|←, →||Rotate clockwise or counter-clockwise around the choosen rotation axis.|
|↑, ↓||Zoom in or out.|
|,, .||Move forward or backward along the Z-axis.|
|⇧ Shift+X||Rotate to the ZY-plane of the current source. (Look along the X-axis of the current source.)|
|⇧ Shift+Y or ⇧ Shift+A||Rotate to the XZ-plane of the current source. (Look along the Y-axis of the current source.)|
|⇧ Shift+Z||Rotate to the XY-plane of the current source. (Look along the Z-axis of the current source.)|
|[ or N||Move to previous timepoint.|
|] or M||Move to next timepoint.|
For all navigation commands you can hold ⇧ Shift to rotate and browse 10x faster, or hold ^ Ctrl to rotate and browse 10x slower. For example, ← rotates by 1° clockwise, while ⇧ Shift+← rotates by 10°, and ^ Ctrl+← rotates by 0.1°.
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 as they can cause out-of-memory exceptions.
Often, it is important to apply transforms estimated with one image to other images in the same space.
If you have moving and target images open in Fiji this script to transform the moving image into the space of the target image. You will need to provide a file containing the saved landmark point pairs.
To manually specify the field-of-view (FOV) of the target space, use this script
To make the scripts above appear in your Fiji Plugins menu, simply copy them into the
/plugins/Scripts folder in your Fiji installation.
- Bogovic, J. A.; Hanslovsky, P. & Wong, A. et al. (2016), "Robust registration of calcium images by learned contrast synthesis", ISBI: 1123-1126, doi:10.1109/ISBI.2016.7493463, <https://ieeexplore.ieee.org/document/7493463>
Publications using BigWarp
- Russell et al. "3D correlative light and electron microscopy of cultured cells using serial blockface scanning electron microscopy" J Cell Sci 130: 278-291 2017.
- Collinson et al. "Correlating 3D light to 3D electron microscopy for systems biology" Current Opinion in Biomedical Engineering 2017 3:49-55
- Lerner et al. "Mycobacterium tuberculosis replicates within necrotic human macrophages" J Cell Biol 2017
- Hildebrand et al. "Whole-brain serial-section electron microscopy in larval zebrafish" Nature 545:345–349 2017.
- Zhang et al. "A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster" Cell 174:3 P730-743.e22, 2018.