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Dockable Views

Dockable Views

All of the dockable Views described in this section can be displayed or hidden using the View -> Dockable Widgets menu. They can be freely moved and aligned to other widgets by dragging and dropping to the different areas of the software. Different predefined alignments are present, however, they can be changed to the users need.


Layer

The Layer view consists of a List containing all layers that are present in the current file. The list is divided into the different layer types (Background, Point, Segmentation, Text, and Binary). It allows selecting which layers are displayed in the main segmentation View by selecting or deselecting the visibility checkbox in front of every Layer name that is possible to be displayed. Additional checkboxes are present to show or hide all layers of a type. A color button is present for Point and Segmentation layers, that allows selecting a new color for the specific shapes or points. The display style can be changed for every Segmentation layer separately using the drop-down menu next to the color button.

The context menu of the layer view allows to delete layers or create new ones. Also, it gives access to export data from specific layers, choose a different layer as background, or copy and past data between slices. It is possible to export the current Layers as a template and import this template in a different file.


Options

The options view provides a way to control the currently selected tool. It is adapted to display different options for the different tools and displays information in the case of the Measurement tool. The actual controls are further described in the Tools section.


Shape Properties

This view displays basic information about the currently selected shape. Also, it allows smoothing the selected shape using the slider on the bottom of this view.


History

It is possible to undo and redo changes that were made to a layer. Furthermore, the creation and deletion of a layer can be undone and redone. To undo or redo an action, either use the menubar Edit->Redo/Undo or use the shortcuts indicated (Undo: Ctrl/Cmd + Z, Redo: Ctrl/Cmd + Y).

The History window can be used to undo or redo multiple actions by clicking at the point that is to be recreated. Actions that can be undone like segmentations using the segmentation tools or changes in the layer window are listed in the history window. If a previous state is recreated using the undo function, the history is not directly affected to allow to redo the actions, however, as soon as a previous state is modified the rest of the history will be removed.


Minimap

The Minimap provides a different View of the data in the current file. Segmentation layers that are selected to be visible in the Layer view are displayed along a chosen axis. There are different modes to display the volume. The default one (Mean) averages the segmentations, the opacity in the minimap corresponds to the mean value along the chosen axis. In Min and Max mode, instead of the average, the minimum and maximum values are chosen, again the opacity corresponds to the observed value. The axis can also be changed (YZ/XZ/XY Planes) to correspond to a specific plane in the volumetric data. Additional options allow to normalize the image and show or hide the background image.

By clicking or dragging on the Minimap the currently selected slice can be changed. The direction will change according to the plane that is selected.


Masked View

The Masked View is a representation of the averaged volumetric data, where only values are considered that contained in a segmentation layer that was set visible in the Layer View. This allows to only observe regions of special intrest. For OCT images, there is a special option to select a band around an edge in the segmentation using the "Select Flattening Mask" Button. Note that this only works if there is a line present in the segmentation layers that spans across the entire volume. If an edge of a shape is selected that is not present in all slices, the result might be misleading.


File Information

The File Information view lists different general properties of the currently open file. It also displays information about all the layers in the file. As this information must be extracted from the original file which might be slow for big files, it is recommended to only display this view when really needed.


Onscreen Keys

The onscreen keys provide basic functionality that might otherwise not be accessible when no physical keyboard is present. The Left and Right keys serve to switch between slices. The Ctrl key is especially useful to switch between drawing and erasing for the different tools.


Toolbar

The toolbar gives access to the different Tools that can be used to segment and annotate data. In addition to the tool selection, it displays and allows to change the scale of the current view using a drop-down menu. The second drop-down menu can be used to rearrange open files. Possible arrangements are tabs (the default), where only one file is showed simultaneously, grid, where files are arranged in a grid and horizontal/vertical.