Getting Started with VVDViewer - JaneliaSciComp/VVDViewer Wiki

Parts of the VVD User Interface

  1. Main Tool Bar: Lets you open files, projects, meshes, analysis window, etc.
  2. Workspace Panel: Lets you select which channels to show in the Render View window.
  3. Record/Export Panel:
  4. Output Adjustment Panel: Lets you adjust brightness and contrast for each channel.
  5. Depth Adjustment Slider:
  6. Render View Settings: Lets you choose how channels are combined, change background color of image, add a legend, save the image as a .tif file, and more.
  7. Render View Window: The 3D image appears here. You can zoom, rotate, or reposition the image using the mouse and command key.
  8. Rotation Slider: Lets you rotate the image in the Render View window.
  9. Channel Properties:
  10. Zoom Slider: Lets you zoom in on the image in the Render View window.
  11. Clipping Panes Panel:

Opening Files

VVDViewer supports 3D and 4D datasets. You can load image slices (tif), image stacks (tif stack, nrrd, h5j, czi, lsm, oib, oif), meshes (obj, swc, ply) and chunked resolution pyramids (vvd, n5).

To load data into VVD, do one of the following:

Drag and drop files into the Workspace panel in the upper left corner of the window.

Click "Open Volume". "Open Project", or "Open Mesh" on the Main Tool Bar.

Or select "Open Volume", "Open Project", or "Open Mesh" from the dropdown File menu.

Changing How Data Are Displayed

Selecting which data are displayed in the Render View window

You can hide or reveal different channels or groups by double-clicking on the lightbulb next to the item in the Workspace panel. When lightbulb is black, channel/group is hidden. In the example below, only the red and blue channels of Group 1 are displayed in the Render View.

Choosing How Channels Are Combined

Use the radio buttons at the top of the Render View panel to determine how channels are displayed.

Left side of Render View toolbar

  • Layered: Channels are layered on top of each other, obscuring lower channels
  • Depth: All channels are rendered at once according to depth in the stack, so more superficial objects obscure deeper objects
  • Composite: Channels are rendered individually and then blended, so deeper features can be seen

Adjusting Image Brightness and Contrast

2D brightness and contrast adjustments are made in the Output Adjustment panel and are applied on top of a 3D rendered image. The parameters are set independently for each color (RGB).

If the Link checkbox is selected, each parameter is set to the same value on all channels within a group.

The 2D parameter values are shared within a group of images. If you want to use different 2D parameters, create a new group in Workspace panel by dragging and dropping the channel outside the group.

small GUI 2

Select Easy Mode to adjust brightness and contrast at once.

If you need more flexibility, deselect Easy Mode. This allows you to adjust gamma, luminosity, and equalization.

Gamma(Gam): used to increase the visibility of dimmer signals

Luminosity (Lum): adjusts the brightness of all signals

Equalization (Eql): makes dimmer signals brighter, but it is less useful than Gam/Lum in most cases. It is most useful for equalizing brightness across time points in 4D data sets.

Zooming In and Out

You can zoom in or out on the image in the Render View panel by:

  • Using the slider on the right side of the Render View panel
  • Clicking and Dragging on the Render View panel using the right mouse button
  • Using the mouse scroll wheel when cursor is on Render View panel
  • Typing a zoom amount in the box at the bottom of the Zoom slider

Zoom slider

The percent zoom is shown in a box at the bottom of the Zoom slider.

You can set the current zoom level as the default by clicking "Save as Default" under the Zoom slider. You can then return to that zoom level by clicking the "Reset" button.

Rotating 3D images

You can rotate the 3D image by:

  • clicking the left mouse button and dragging with the cursor positioned on the image
  • dragging or clicking a position on the X, Y, and Z sliders at the bottom of the Render View window
  • typing numbers into the X, Y, and Z boxes at the bottom of the Render View window

Rotation sliders

To rotate the image in 45-degree increments, select the "45 increments" checkbox to the right of the rotation sliders.

To return to the original position, click "Reset to 0" to the left of the rotation sliders.

To see the center of rotation on the rendered image, click the "Center" checkbox at the top of the Render View panel. This is helpful when creating movies, but it should be unchecked if you don't want it to appear on a captured image or movie.

Center checkbox indicated on Render View panel

Repositioning image in Render View panel

To drag the image in the Render View window, hold down the Command key and left mouse button while dragging cursor on the window.

Changing Image Quality and Smoothing

Image quality can be altered using the Quality drop-down list in the Render View Settings panel.

To smooth the image, check the Intrp box in the Render View Settings panel. With the box checked, trilinear interpolation is used to smooth the image; with it unchecked, you actual voxel values are used.

Changing 3D Projection Mode

The slider marked "V. AOV." lets you change the 3D graphical projection mode. With the slider all the way to the left ("Ortho" for orthographic), everything is the same size, regardless of depth. It is good for scientific visualization with a scale bar.

Sliding the slider to 30 or 45 degrees creates a cabinet projection in which closer objects are larger than farther away objects. It is good for sensing object depth in movies.

3D Projection Mode Setting

Fly-Through Mode

When the FreeFly checkbox is checked, the image appears as if the camera is inside your sample. The user can check the 3D object from inside.

FreeFly Checkbox

Changing Background Color

The background color of the Render View window can be changed by clicking on the color bar next to "Background" in the Render View Settings toolbar. You can choose grayscale or color backgrounds.

Changing the background color

Adding a Legend

To add a legend to the Render View image, click "Legend" in the Render View Settings toolbar. This opens a window that allows you to choose which channels you want to indicate in the legend. Click the left circle at the top of the Legend window to close it. The legend will appear on exported images.

Adding a Legend to Image

Exporting Render View Image

To save the current Render View image as a .tif file, click "Capture" on the Render View Settings toolbar.

Capture image button