Graphical user interface

Image Panel

The Image Panel is the primary area for displaying the field of view (FOV) of the image and objects contained within the image. The Image Panel provides zoom control buttons for manipulating the display of the FOV in the zoombar. There are four (4) modes of display that can be accessed via the zoombar:

• Main View (2D View) shows the displayed image in 2D; for multi-dimensional images, you can navigate to a different time point (t-frame) or plane (z-frame) using the T and/or Z bar(s) below the image.
• 3D View shows the displayed image in 3D; this option is only available when there is more than one z-plane on the image.
• 3D Plane View shows an xy-, yz-, and xz-plane of the image as well as a 3D view simultaneously; this option is only available when there is more than one z-plane on the image.
• VR View shows the displayed image in Virtual Reality (VR) space; while this mode is active, you will not be able to interact with the displayed image in the Image Panel.

You can interact with the image directly by moving your mouse cursor to the image and using the mouse to manipulate the display. For more information, please refer to the document on mouse interactions.

3D View Selection Modes

Selection modes are options which help the user select their data in the viewer with different formats depending on their wants and needs. A few selection modes are available and are described below. These options are useful because there are some objects in Aivia which do not have visual representations. Neuron, Dendrite, Spine, Cell, Cytoplasm, and Nucleus are all "Non-Visual" meaning while they are considered objects that are measurable, the representation seen in the viewer is through another objects visual display. For example, a Cell is visually displayed by the Cell Membrane border, Neuron is displayed by the collection of Soma + Dendrite Segments + Spine Heads/Necks, etc

• Whole Cell
  • When selecting a component of a "Cell" hierarchy, the entire Cell Hierarchy will be selected. The Cell Hierarchy select-able from the viewer includes, Cell Membrane, Nuclear Membrane, and/or any vesicle with a parent object.
• Whole Tree
  • When selecting a component of a "Neuron" hierarchy, the entire Neuron Hierarchy will be selected. The Neuron Hierarchy select-able from the viewer includes, Soma, Dendrite Segments, Spine Necks, and/or Spine Heads
• Sub Tree
  • When selecting a component of a "Neuron" hierarchy, any data down stream of the selected object will be selected. For example selecting a Dendrite Segment will select the Dendrite parent of the Dendrite Segment and all Segments
• Spines
  • When selecting a Spine component, the Spine Head and Spine Neck are selected.
• Single Item
  • Selects only the item clicked

Contents Panel

The Contents Panel consists of several major features for displaying contents, editing analysis data, and exporting videos. It can be resized vertically by dragging the blue dotted handle near the top middle of the panel or collapsed/expanded by clicking once on the same handle. Alternately, you can open the panel by clicking on the button for a specific tool to open that particular feature. Some features are unavailable in different view modes.

There are six (6) tools in the Contents Panel:

• The Image Explorer displays thumbnails of the images you have loaded into Aivia and lets you switch between the loaded files
• The Annotations tool provides a set of on-screen tools for manually measuring the displayed image in Main View (2D View).
• The Outline Editor lets you create and edit the outlines of select objects in Main View (2D View).
• The Track Editor lets you edit track objects, modifying the relationships between tracks and track points over time.
• The Spreadsheet displays the measurement data for objects and object sets.
• The Video Animator lets you create and export flythrough videos in 3D View by capturing individual keyframes containing information about the current display.

Analysis and Display Panels

The primary tools for controlling the display of channels, objects, and other display overlays on the image are found in the following display settings panels:

• The Channel Settings panel lets you adjust the visibility, contrast, brightness, color, and rendering mode of the channels on the loaded image.
• The Object Settings panel lets you adjust the visibility, color, and display style of objects and tracks on the loaded image.
• The Clipping & Ortho Planes panel lets you add clipping planes or ortho slices to the 3D display to hide parts of the rendered volume or objects.
• The Tags panel lets you create, edit, and adjust the visibility of tags, which are customizable labels with notes for locations of interest in the image.

There are five (5) tools within the Analysis Panel:

• The Recipe Console is the tool displayed by default; the Recipe Console allows you to select and apply an automated image processing and analysis pipeline (called a "recipe") to an image.
• The Image Enhancement Tool allows you to select and run an image processing pipeline to enhance an image.
• The Charts tab lets you plot analysis results graphically with a variety of display options.
• The Pixel Classifier lets you enhance an image using Aivia's patented machine learning technology for content-aware enhancement of image features.
• The Object Classifier lets you create and apply user-guided or automatic object classifications on detected objects.

Panel viewing controls

You may resize the Image Panel, Contents Panel, and any of the Analysis and Display Panels using the blue dotted handles. Click on the blue dotted handles that have blue arrows to hide/reveal panels. 

The Analysis and Display Panels can be hidden and shown, collapsed and expanded, pinned and unpinned, and docked and popped out into floating windows with the global panel controls as well as controls found in the header of each panel.

Global panel controls

The global panel controls are found at the top of the Analysis and Display Panels section when panels are docked and along the right side of the Aivia window when all panels are in floating windows or not selected for display.

A description of each global panel control is given in the table below.

Saving and restoring layouts

Your preferred layouts of the Aivia GUI can be saved and restored as layout presets. Click on the Open Advanced GUI Options icon to open a menu where you can save, restore, rename, and remove layout presets (see diagram below). 

Toggling panel display

To remove or restore the display of any Analysis and Display Panel, click on the Open Advanced GUI Options icon and then on the name of the panel you wish to hide or show in the Displayed Items column. Panels that are displayed are outlined in blue in the Displayed Items column.

Panel header controls

The panel header controls for each panel are found in the same box as the panel name (see figure below). The panel header controls apply only to the associated panel.

Each option in the panel header is described in the table below. Some options are not available in certain layouts.

Docking and undocking panels by drag and drop

You can left-click and drag a panel header away from the main Aivia window or a floating Aivia Controls window and then drop the panel to move it to its own floating window. To dock a panel, you can left-click and drag the panel header to the Analysis and Display Panels region in the main Aivia window or to a floating Aivia Controls window, wait until the region turns blue and the docking icon appears, and then drop the panel to dock it in that location (see example above). You can dock all panels in a floating window by dragging the header of the Aivia Controls window. You can also return all panels in an Aivia Controls window to the main Aivia window by clicking on the 'X' in the upper-right corner of the Aivia Controls window.

Related articles

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