| Mode | What gets rendered |
|---|---|
| Fused | All active (checked) sources overlaid |
| Source | Only the current (radio-selected) group |
When multiple images are loaded, each image's channels appear as a named group in the Groups panel. Two controls are available per group:
- Radio button: selects the current group. In Source display mode, only the current group is rendered, allowing you to inspect each image in isolation. Switching radio buttons toggles between images
- Checkbox: toggles group activity (visible/hidden). In Fused display mode, unchecking a group hides all its channels from the render. With both checkboxes checked, both images are overlaid simultaneously
The Source Transforms card provides controls for multi-image transform management:
| Control | Description | |
|---|---|---|
| Save Transform | Saves the current transform of a selected group to an XML file | |
| Load Transform | Loads a previously saved XML transform and applies it to a selected group | |
| Export Transformed Image | Applies the manual transform of a selected group to its image data and writes the resampled result to a 16-bit TIFF file. See Exporting the Registered Image |
Use the mouse to rotate the scene to a viewpoint where the misalignment is clearly visible. Use Fused mode (both groups checked) to overlay both images.
In the Sources panel, click the radio button next to any channel of the moving image (Group 2) to make it the current source.
Press T to enter BVV's manual transform mode. A message appears in the viewer confirming the mode is active. In this mode:
- Left-drag: rotates the current source
- Right-drag / scroll: translates the current source
- All other channels in Group 2 should follow automatically via Live Sync (Source Transforms panel)
With Fused mode active and both groups checked, move the moving image until it overlaps the reference. Toggle between Fused and Source display modes to check alignment from both images' perspectives.
Press T again to exit manual transform mode and lock the current position. The transform will be applied to the other channels in the group.
Open the Source Transforms panel and click Save Transform. Select Group 2 (the moving image) when prompted and choose a save location. The transform is saved as an XML file:
Click Load Transform in the Source Transforms panel, select the XML file, and the transform will be applied to the matching group.
Export Transformed Image bakes the manual transform into pixel data by resampling the moving image onto a chosen target grid, producing a standard TIFF. The result is saved as a 16-bit TIFF.
A two-choice prompt appears:
Select the group whose manual transform you want to apply. This is the image that was moved during registration (Group 2 in the two-image workflow above). Its current transform (the full composition of the calibration (pixel size) transform and the manual registration transform) is what gets baked into the output.
Select the group that defines the pixel grid of the output file: its dimensions, voxel size, and spatial extent. The moving image is resampled so that every output voxel corresponds to the equivalent world-space location in the reference.
Choosing the reference image (Group 1) as the target grid is the standard choice: the result is a new volume of the moving image in the same coordinate frame as the reference.
Choosing the moving image itself as the target grid resamples the transformed data back onto its own original grid. It is effectively a sanity check that produces a transformed copy at the moving image's native resolution.
| Key | Action |
|---|---|
| T | Enter manual transform mode for the current source/group |
| T again | Commit transform and exit |
| Esc | Abort (discard changes) |
| Action | Normal | Fast (Shift) | Slow (Ctrl) |
|---|---|---|---|
| Rotate left/right | ← → (1°) | Shift+← → (10°) | Ctrl+← → (0.1°) |
| Translate in Z | , / . or scroll | Shift+scroll | Ctrl+scroll |
| Drag rotate | left-drag | Shift+left-drag | Ctrl+left-drag |
| Drag translate | right-drag | ||
| Select rotation axis | Shift + X, Y, Z | ||
| Zoom in/out | ↑ ↓ or Ctrl+Shift+scroll | Shift+↑↓ | Ctrl+↑↓ |
- 0.1° increments: use Ctrl+← →: the finest rotation step available
- Lock rotation axis: press X, Y, or Z to constrain keyboard rotation to a world axis before nudging with arrow keys
- Align to principal plane first: use the view alignment shortcuts (Shift+Z, Shift+X, Shift+Y) to snap to XY/XZ/ZY before entering T-mode — gives a clean, predictable starting orientation
- Fine translation: hold Ctrl while right-dragging for slower, more controlled panning
- Adjust render quality (Scene Controls → gear menu) to Low for faster interaction during alignment, then switch to High for final inspection.
- The Reset view button in Scene Controls re-centers and re-fits the scene to the viewport at any time.
- Transforms are applied as fixed source transforms: they move the image data in 3D space independently of the camera
- When exporting registered images: When a single source serves as both moving and reference, a transformed copy of itself will be created