Object Settings

Toolbar

The toolbar contains high level actions.

Object Set Tree View

The Object Set Tree View shows all object hierarchies, if any, on the image. The hierarchy of object sets represents different types of objects found on the image, such as Neurons, and all their components, like Somas, Dendrites, and Spines. It also contains any subsets associated with those object sets.

Object Set: 

Object Subset: 

You can control the visibility of any individual object set with the button. The top level object set will toggle the visibility of all the object sets below it, as well as copy any display settings to all child object sets.

You can see the count for the set (n=Count) as well as the percentage of the parent object set. Note that the percentage pertains to the object set that that the subset is under and is not the percentage of the parent object subset (e.g. the percentage of the Affected subset on the right is based on the number of objects in Dendrite Set, and not the number of objects in the Treatment subset)

You can select an object set in this view, and more detailed settings will appear in the Detailed Display Settings area.

Buttons

Each table row in the Display Settings panel represents a single aspect of the currently selected object set or object subset. Each row can be controlled independently to adjust the display settings. There are six (6) basic controls for nearly every object set:

Additional controls that are specific to particular object types are summarized in the table below.

Using the Object Set Settings

The Object Set Settings panel is active whenever you have an image loaded in Aivia. The software automatically populates the table based on the object sets and object types that are in the image file, if there are any.

Display settings in the top level object set in a tree often affect the settings for each object set in its hierarchy. The names of object sets  can be edited after their names are double-clicked in the Display Settings header or in the Object Set Tree View.

Set display visibility

Each object set can be shown or hidden separately with the Toggle Visibility icon to the left of its name. The icon has two states:

For object trees, you can show or hide every object set in the group with the Toggle Visibility icon on top level object set.

Additionally, the right click menu has several options for quickly set the visibility of multiple object sets.

• Show all object sets will set the visibility of all object sets to visible.
• Hide all object sets will set the visibility of all objects sets to hidden.
• Show only "<Clicked Set>" will hide every set except the clicked on set.
• Show only "<Clicked Set>" and its tree will set every child in the tree to visible and every other to hidden.
• Show "<Clicked Set>and its tree will set all child sets in the tree to visible.
• Hide "<Clicked Set> and its tree will set all child sets in the tree to hidden.

Specify object display options that are unique to object types

The options available for displaying object sets and overlays depend on the object types. Please refer to the following pages for more information:

• Tracks
• Meshes (3D)
• Neurons (3D)

Change object set color

You can change the object set color display by clicking on the icon (or colored rectangle) associated with the object set in the Color column. Clicking on the icon will bring up a color picker menu which allows you to specify a different color or different coloring mode. There are seven (5) coloring options:

• Solid color applies the same color to every object in the group
• Color by object type applies the same color to the same type of object (e.g. meshes, dendrites, spines)
• Color by name applies a different color to each object depending on the name of the object
• Color by measurements applies a different color to each object depending on its value for a specified measurement
• Color by cell is specific to neuron and whole-cell objects and applies a different color for each neuron or whole cell

When you click on the icon in the Color column, the coloring option selector appears (see right). To change the coloring type, click on the dropdown menu in the selector.

You can also apply a specific color using the color picker below the dropdown menu. Click or drag the slider on the right to specify the desired hue (color) and click anywhere on the main display to specify the saturation and brightness desired. Alternately, you can specify a color by entering the hexadecimal color code in the textbox below the main display.

Color objects by measurements

When you select the Color By Measurement option, a different coloring selector appears. You can specify the measurement you want to use as well as the color palette and measurement range. The Color By Measurement selector is shown on the right.

Click on Measurement to open a dropdown menu listing all the available measurements that can be used for this coloring mode. Click on a measurement name to select the measurement.

The minimum and maximum values are shown in the slider below the measurement selector. The values are automatically populated based on the minimum and maximum object measurements on the image. You can drag the slider to define the desired value range to color.

Below the value slider is the color palette selector, where you can specify a color gradient for coloring the measurements. Additionally, you can adjust the gradient by dragging each of the color markers or change the color using the color picker below.

Delete object trees

You can delete an object tree by right-clicking on its row and selecting Delete Object Set(s) from the context menu. You will be prompted to confirm deleting the group. This action cannot be undone.