User Interface

Application overview

Colada stores all loaded data in a data repository, called the “scene” (or Colada scene or MRML scene). Each data set, such as an image volume, surface model, or point set, is represented in the scene as a “node”.

Colada provides a large number “modules”, each implementing a specific set of functions for creating or manipulating data in the scene. Modules typically do not interact with each other directly: they just all operate on the data nodes in the scene.

Module Panel

This panel (located by default on the left side of the application main window) displays all the options and features that the current module offers to the user. Current module can be selected using the Module Selection toolbar.

Data Probe

Data Probe is located at the bottom of the module panel. It displays information about view content at the position of the mouse pointer:

Slice view information (displayed when the mouse is over a slice view):
- Slice view name: Red, Green, Yellow, etc.
- Three coordinate values, prefixed with +-X,+-Y,+-Z.
- View orientation: XY, YZ, XZ and Reformat for any other orientation.
- Slice spacing: distance between slices in this orientation.
Volume layer information: three lines, one for each volume layer
- Layer type: L (label), F (foreground), B (background).
- Volume name, or None if no volume is selected for that layer.
- Volume voxel (IJK) coordinates.
- Voxel value. For label volumes the label name corresponding to the voxel value is also displayed.
Segmentation information: for each segmentation visible at that position
- Layer type: S (segmentation)
- Segmentation name.
- Segment names. Multiple segment names are listed if multiple segments are displayed at that position (the segments overlap).

Views

Colada displays data in various views. The user can choose between a number of predefined layouts, which may contain slice, 3D, chart, and table views.

The Layout Toolbar provides a drop-down menu of layouts useful for many types of studies. When Colada is exited normally, the selected layout is saved and restored next time the application is started.

Application Menu

File: Functions for loading a previously saved scene or individual datasets of various types, and for downloading sample datasets from the internet. An option for saving scenes and data is also provided here. Add Data allows loading data from files. Save opens the “Save Data” window, which offers a variety of options for saving all data or selected datasets.
Edit: Contains an option for showing Application Settings, which allows users to customize appearance and behavior of Colada, such as modules displayed in the toolbar, application font size, temporary directory location, location of additional Colada modules to include.
View: Functions for showing/hiding additional windows and widgets, such as Extensions Manager for installing extensions from Colada app store, Error Log for checking if the application encountered any potential errors, Python Console for getting a Python console to interact with the loaded data or modules, show/hide toolbars, or switch view layout.

Status bar

This panel may display application status, such as current operation in progress. Clicking the little X icons displays the Error Log window.

Data trees

Data trees are dedicated to work with geological data. Clicking on checkbox makes this data visible in Data module and thus can be viewed on the views. Right click on items invokes pop-up menu with allowed actions on selected items. Right click on tree header also invokes pop-up menu with different actions available.

Scene filter

Scene filter may be used to filter (hide) nodes whoose attribute’s value doesn’t match the value in the input line. The same can be done by setting Domain in the combo box. Node attributes can be viewed in Data module.

Mouse & Keyboard Shortcuts

Generic shortcuts

Shortcut	Operation
`Ctrl` + `f`	find module by name (hit `Enter` to select)
`Ctrl` + `o`	add data from file
`Ctrl` + `s`	save data to files
`Ctrl` + `w`	close scene
`Ctrl` + `0`	show Error Log
`Ctrl` + `1`	show Application Help
`Ctrl` + `2`	show Application Settings
`Ctrl` + `3` / `Ctrl` + `	show/hide Python Console
`Ctrl` + `4`	show Extensions Manager
`Ctrl` + `5`	show/hide Module Panel
`Ctrl` + `h`	open default startup module (configurable in Application Settings)

Slice views

The following shortcuts are available when a slice view is active. To activate a view, click inside the view: if you do not want to change anything in the view, just activate it then do right-click without moving the mouse. Note that simply hovering over the mouse over a slice view will not activate the view.

Shortcut	Operation
`right-click` + `drag up/down`	zoom image in/out
`Ctrl` + `mouse wheel`	zoom image in/out
`middle-click` + `drag`	pan (translate) view
`Shift` + `left-click` + `drag`	pan (translate) view
`left arrow` / `right arrow`	move to previous/next slice
`b` / `f`	move to previous/next slice
`Shift` + `mouse move`	move crosshair in all views
`Ctrl` + `Alt` + `left-click` + `drag`	rotate slice intersection of other views (`Slice intersections` must be enabled in `Crosshair selection` toolbar)
`v`	toggle slice visibility in 3D view
`r`	reset zoom and pan to default
`g`	toggle segmentation or labelmap volume
`t`	toggle foreground volume visibility
`[` / `]`	use previous/next volume as background
`{` / `}`	use previous/next volume as foreground
`left-double-click`	maximize view/restore view layout

3D views

The following shortcuts are available when a 3D view is active. To activate a view, click inside the view: if you do not want to change anything in the view, just activate it then do right-click without moving the mouse. Note that simply hovering over the mouse over a slice view will not activate the view.

Shortcut	Operation
`Shift` + `mouse move`	move crosshair in all views
`left-click` + `drag`	rotate view
`left arrow` / `right arrow`	rotate view
`up arrow` / `down arrow`	rotate view
`End` or `Keypad 1`	rotate to view from anterior
`Shift` + `End` or `Shift` + `Keypad 1`	rotate to view from posterior
`Page Down` or `Keypad 3`	rotate to view from left side
`Shift` + `Page Down` or `Shift` + `Keypad 3`	rotate to view from right side
`Home` or `Keypad 7`	rotate to view from superior
`Shift` + `Home` or `Shift` + `Keypad 7`	rotate to view from inferior
`right-click` + `drag up/down`	zoom view in/out
`Ctrl` + `mouse wheel`	zoom view in/out
`Ctrl` + `b`	toggle tilt lock
`+` / `-`	zoom view in/out
`middle-click` + `drag`	pan (translate) view
`Shift` + `left-click` + `drag`	pan (translate) view
`Shift` + `left arrow` / `Shift` + `right arrow`	pan (translate) view
`Shift` + `up arrow` / `Shift` + `down arrow`	pan (translate) view
`Shift` + `Keypad 2` / `Shift` + `Keypad 4`	pan (translate) view
`Shift` + `Keypad 6` / `Shift` + `Keypad 8`	pan (translate) view
`Keypad 0` or `Insert`	reset zoom and pan, rotate to nearest standard view
`left-double-click`	maximize view/restore view layout

Note: Simulation if shortcuts not available on your device:

One-button mouse: instead of right-click do Ctrl + click

Trackpad: instead of right-click do two-finger click

Python console

The following shortcuts are available in the Python console.

Shortcut	Operation
`Tab`	auto-complete
`up arrow` / `down arrow`	command history
`Esc`	clear selection, return to current command line, clear current command line
`Ctrl` + `g`	run Python script from a file
`Ctrl` + `v`	paste Python script from clipboard and run it

Note that when code is pasted into an empty line then all the code in the clipboard is executed at once. If the current command line is not empty then the code from the clipboard is pasted into the console and executed line by line. When code is executed line by line, the behavior is different in that an empty input line immediately closes the current block, and output is printed after executing each line.