Channel Settings

Channel Settings is one (1) of the four (4) display settings sections. This section lets you adjust the appearance of each channel 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 Channel Settings panel is at the top of the column to the right of the Image Viewer by default. The Channel Settings table header contains controls that apply to the whole image, and each table row contains controls that apply to just the corresponding channel. An example of the Channel Settings table is shown below.

Table header

The table header contains labels for each column as well as global display options for the image. The three (3) buttons in the table header are the following:

Table row

Each table row in the Channel Settings table represents a single channel on the displayed image. The background color of each row corresponds to the specified channel color in the Color column of the table. Each row can be controlled independently to adjust the display settings of each channel. There are five (5) controls:

Using the Channel Settings panel

The Channel Settings are active whenever you have an image loaded and displayed in Aivia. The software automatically populates the table based on the number of channels that are on the image and the channel color(s).

Apply Channel Display Color

This function sets the display color of each channel to a color that is based on a color map selected by the user. The color maps are predefined such that when applied, each channel's display color is different from its neighboring channel(s). 

There are two types of color maps available: Discrete and Gradient.

• Discrete color maps assign a color to each channel that is distinctly different from its neighbors' color. This type of color maps helps to differentiate adjacent channels more easily.
• Gradient color maps assign a color to each channel such that each color is a gradual change from one end of the color spectrum to the other.  This type helps to identify the channel names by color shown in the image viewer.

To apply a color map, click on the icon to display the list of available color maps. Click to select the desired color map, and the channels colors will be updated accordingly.

Additionally, there is an option to reverse the order of the colors assigned to each channel. Click on  the icon to display the list of available color maps, the click Reverse Channel Colors. The colors assigned from the first to the last channel will then be applied from the last to the first channel, thus reversing the order of assignments.

Set channel visibility

Channels can be shown and hidden individually with the Show/Hide Channel icons to the left of their names. The Show/Hide Channel icon has two states:

Additionally, you can show/hide all channels by clicking on the Show/Hide All Channels icon in the table header.

Change render mode

You can specify the rendering mode for channels in 3D View by clicking on the icon in the View column. Clicking on the icon will bring up a list of render mode options that are available for the selected item. There are three (3) options:

Rendering Mode	Icon	Description
Maximum Projection		Sets rendering to Maximum Intensity Projection mode
Composite Volume		Sets rendering to Composite Volume mode
Preview Surface		Sets rendering to Preview Surface mode

Once a new rendering mode is selected, the displayed image refreshes automatically to reflect the new selection.

A comparison between the three (3) rendering modes is shown below.

Change channel color

You can change the channel color display by clicking on the icon (or colored rectangle) associated with the selected channel in the Color column. Clicking on the icon brings up a color picker menu, which allows you to specify a color. 

The Basic Color Picker (see right) is the default color picker, which presents a number of standard colors to choose from.

When you click on the Advanced button on the Basic Color Picker, the Advanced Color Picker will be shown (see right). 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.

Additional LUT mapping and color options are available in the Advanced Coloring menu, which is found in the right-click menu of each channel-name cell in the Channel Settings table. The Advanced Coloring > LUT Mappings menu contains a variety of LUT mappings that you may choose from.

Change display brightness

You can adjust the displayed brightness of channels using the lookup table (LUT) function built into the Channel Settings. An LUT control is circled in red to the right. There is one (1) pair of controls for each channel. When you hover over a control, the cursor changes into a left-right arrow, and you can click and drag the control to the left or right to modify the displayed dynamic range. This action does not alter the pixel/voxel values on the image, merely the brightness of the displayed image.

You can also set the LUT to update automatically by clicking on the Auto-fit LUT icon . When toggled on, the brightness of the displayed image is determined by the dynamic range (minimum pixel intensity to maximum pixel intensity) of the current frame.

Show expanded LUT

You can click on the Expand icon  on the far left side of a table row to show the expanded LUT or ISO level, depending on the selected rendering mode.

Expanded LUT

You will see the expanded LUT if you have either the Maximum Projection or Composite Volume rendering mode selected. An intensity histogram is shown indicating the frequency of each intensity level.

The expanded LUT mode gives you finer control over the minimum and maximum dynamic range values. You can double-click on the dotted line to add another LUT Adjustment Point, which can be clicked and dragged for tuning of the LUT.

ISO level

The ISO level display is shown when you have the Preview Surface rendering mode selected. The ISO Level sliders and textboxes let you specify the minimum and maximum intensity levels for mesh generation. This is the main control for adjusting the display in Preview Surface mode.

Channel Groups

Channel groups can be utilized to manage multiple channels simultaneously, offering a streamlined approach to handling numerous channels effectively. This can help keep work organized by logically grouping related channels, which is particularly useful in complex workflows.

Channel groups can be created and managed at the top of the panel: . The plus icon creates a new, empty channel group. The reset icon loads channel groups created within LASX if they are available with the saved image. 

Channel group names can be changed by clicking on the name. Channels can be added or deleted from a group, by de/selecting them from a drop-down menu. The visibility of all channels in a group can be switched by clicking on the "eye" icon. The channel group can be deleted by the "trash" icon.