5. Start the registration

The main window shows the selected image with the atlas overlay.

Dataset DOI: 10.25493/G6CQ-D4D

Note

If necessary, change the atlas from coronal view to sagittal or horizontal view (see Navigation panel below)

1. Move the atlas to the approximate position of your section using the yellow dots in the three small windows from the navigation panel.

2. Start anchoring by placing a marker with the “Space bar” , it is initially a cross, and it is the fix point of (most) transformations. The “Escape key” can be used to remove the marker.

3. The main window supports mouse drag in multiple modes in order to stretch the atlas and find the correct position.

If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation).

Note

The panel can be resized towards the left (common border with Control Panel) and towards the bottom (common border with Filmstrip).

4. Save the position by pressing “Store”. The registration is copied to the remaining slides to help with scaling (visible also in the filmstrip)

5. Go through all sections and refine position and cutting angles.

Note

When jumping from one section to the other, wait a few seconds for the image to load

Note

The “restore” button allows you to go back to the saved position if necessary

6. Save your results in the descriptor file (.waln) by pressing “Save to bucket”.

7. When the registration is finished, you can export your descriptor files ( .seg files used for analysis in the QUINT workflow) by pressing “export overlays”. All results are zipped and stored in the bucket. The result file name will be the same as the one chosen to create the registration, e.g. “my-registration.zip”.

6. Short keys

To do this	Press	Description
Place marker	Space bar	Markers are the anchor points of most transformations (stretch and rotate)
Remove marker	Esc	Removes a previously placed marker
Horizontal stretch from maker	Left/Right arrow keys	Marker becomes a vertical line, mouse drag horizontally resizes the cut
Vertical stretch from maker	Up/Down arrow keys	Marker becomes a horizontal line, mouse drag vertically resizes the cut
Rotate around marker	PgUp/PgDown	Marker becomes a cross with a surrounding arc, mouse drag rotates the cut
In plane adjust	Click + drag	If there is no marker, or the marker is a cross, mouse drag slides the cut in its plane (translation)

7. Control panel

Button	Function
Store	Store the current alignment and propagate to unaligned sections (Note this does not save the series to your bucket)
Restore	Reset the current alignment to the last stored position
Clear	Reset the current alignment to the default position
Overlay Slider	Opacity of the atlas overlay, when fully opaque, it becomes an outline
Overlay color	The outline color
Filmstrip slider and color	The above settings, applied to the filmstrip
Save to bucket	Save the series to your bucket (and overwrite the existing file)
Export overlays	Generates a series of .flat files (for Nutil or similar utility), and stores them into a .zip file in the bucket (re-using the name of the series descriptor, e.g. series13.json will export series13.zip)

Note

The right border of the control panel can be dragged horizontally, allowing to resize the panel and the main view

8. Filmstrip

Drag horizontally to see series, click on a section in order to load it into the main view. The top border of the filmstrip can be dragged vertically, allowing to resize the panel and the main view

9. Navigation panel

Shows the three standard planes centered around the midpoint of the current alignment visible in the main view.

The rectangle of the current cut is projected on each standard plane as a yellow line/rectangle/parallelogram. A small yellow circle represents the midpoint of the projection.

Drag the midpoint around to move the cut.

Drag anywhere else to rotate the cut (inside the given standard plane, around the midpoint)