Object Settings

Object Settings is one (1) of the four (4) display settings sections. This section lets you adjust the appearance of each object set, as well as any additional overlay options, on the currently displayed image. The adjustments applied here only change how the image is shown in the Image Viewer and do not change the underlying data on the image.

Interface

The object settings display can be broken up into 3 sections, the Toolbar area, the Object Set Trees area, and the Display Settings area.

On this page:

The toolbar contains high level actions.

Name	Icon	Description
Collapse All		Collapses all object sets in the tree view.
Expand All		Expands all object sets in the tree view.
Create Object Set Templates		Creates empty object set trees. Opens a menu from which you can select to create an empty outline, mesh, or neuron set. You may choose to add objects created with the Outline Editor or 3D Tools to these sets, for example.
Copy Selected Objects		If any objects selected, copies selected objects into a new object set structure like the existing one, an existing object set structure that's similar (e.g. neurons into neurons), or any mesh based objects into a standalone mesh object set.

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.

Display Settings

In the display settings, you can see all the display settings for the object set or subset currently selected in the Object Set Tree View. Depending on what's selected, and what type of objects it contains, you may see different settings.

Outlines 2D

Tracks 2D

Meshes 3D

Dendrites 3D

Subsets

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:

Name	Icon	Description
Toggle Visibility		Shows or hides the object set from view
Load Recipe Settings		Loads the recipe settings and parameters used to generate this object set into the Recipe Console. It's grayed out if the object set was not made using the recipe console. Only available on the top object set in an object set hierarchy.
Export Objects to a Mask		Exports the objects to a mask or channel; You may export to the following: 8, 16, or 32 bit binary mask. The exported objects will have the maximum intensity for pixels/voxels contained by the objects and zero (0) for pixels/voxels outside of all objects in the set. 8, 16, or 32 bit labelled mask. The exported pixels/voxels have intensities that correspond to the objects that contain them and have an intensity of zero (0) if they are outside of all objects in the set. 8 bit masks will allow a max of 255 unique objects labels. 16 bit masks will allow a max of 65535 unique object labels. 32 bit masks will allow a max of 2147483647 unique object labels. 8, 16, or 32 bit binary channel. Same behavior as exporting to a binary mask, except the mask is added as a channel to the existing image. This is useful to convert an object set into an input image for training or recipe apply.
Select Object Color Scheme		Specifies the coloring mode for the object set
Select Object Transparency		Specifies the percent transparency of the object set.
Select Rendering Mode		Specifies the rendering mode of the object set in 3D View; the available options are the following: Solid Surfaces renders meshes as solid, closed surfaces Wireframes renders meshes as sets of connected line segments Points renders meshes as point clouds

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

Object Type	Name	Description
Dendrites	Select Dendrite Display Mode	Specifies the display style for dendrite display, there are three (3) options: Surface shows the dendrite as a full-formed surface Sphere shows the dendrite as a thin trace connected by spheres with radii determined by the dendrite detection Line shows the dendrite as a thin trace
Tracks, Spots	Set Overlay Radius	Specifies the radius of the overlay display; this can be applied to tracks, anchors, trends, and spots
Tracks	Set Track Length	Specifies the number of frames to display with the track overlay; a longer track length may result in reduced performance
	Show/Hide Track Labels	Shows/Hides track labels in Main View (2D)
	Select Anchor Display Mode	Specifies the display style of the anchor overlay; there are two (2) options: All shows all anchors on the displayed portion of a track Current shows only the anchor for the current position of the track
	Set Trend Display Mode	Specifies the display style of the trend overlay; there are three (3) options: Full Track shows the trend from the first to the final frame of a given track First To Current shows the trend from the first frame to the current frame Only Visible shows the trend from the earliest visible frame, based on the track length specified, to the current frame