This page explains how to create and export still images and movies for publication and presentation.

Creating Still Images for Presentation

Annotating the Image in the Render View Window

Adding a Legend

To add a Legend to the image, click Legend at the top of the Render View panel. This opens a small window that lists the channels currently displayed in the window. Use the check boxes to select which channels you want to appear. To change channel names, left-click on the channel name in the Workspace panel and type a new name.

The font, size, and color of the Legend text can be set in the Properties tab of the Settings window

Adding a Scale Bar

Before adding a scale bar, make sure the numbers in the X, Y, and Z text boxes at the bottom of the Properties panel contain the correct voxel dimensions in microns.

To add a scale bar to the image in the Render View window, click SclBar atthe bottom of the Properties panel. If you want the scale bard labeled with the length, check Text. Type the desired length of the scale bar to be in the text box, and select units from the unit drop-down list. Select the number of decimal places using the "Digit" drop-down list. If you check "Fix Length", the length of the bar in the Render View window will remain the same as you zoom in and out, so the number of units it represents will change. With the box unchecked, the number of units represented will remain the same as you zoom, so the length of the bar on the screen will change.

The font, size, and color of the scale bar text can be set in the Properties tab of the Settings window

Note: If you are creating a figure with a scale bar, make sure the V. AOV slider is all the way to the left ("Ortho"), so all structures are displayed at the same scale, regardless of depth.

Changing the Background Color of the Image

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 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.

Exporting the Image in the Render View Window

To save the current Render View image as a .tif file, click Capture on the toolbar at the top of the Render View panel.

Recording and Exporting Movies

The Record/Export panel enables you to animate certain aspects of a volume within the rendering view and export the movie as a .mov file to use in presentations, etc..

Note: When making movies, it may be helpful to have your object's center of gravity in the center of the render view window. You can mark the center of the Render View window by checking the Center checkbox at the top of the panel. After positioning your volume as desired, deselect the checkbox to avoid having the center mark appear in your movie.

Basic Movies

The operations available under the Basic tab of the Record/Export panel include rotation around the X, Y, or Z axis, time frame progression (from a set of volumes organized as the same tissue over time), and alternation between a set of differing volumes.

Rotation Movies

If you check the Rotation box, you will construct a movie in which the volume in the Render View window is rotated around the X, Y, or Z axis. The default is Y. The number in the “Degrees” text box is the total number of degrees the volume will be rotated during the movie. The number of degrees of rotation from one frame to the next depends on what you type in the Movie Length and FPS (frames per second) boxes.

Two options are available for rotation speed control.
• Linear. The rotation speed is constant from the beginning to the end of a movie.
• Smooth. The rotation accelerates and then decelerates through the movie.

If the Rewind box is checked, the movie will rotate the volume back and forth between the starting and end rotation angle. For example, if the number in the "Degrees" box is 45, the movie will show rotation as follows: 0 → 45 → 0 → -45 → 0 degrees.

To view your movie, simply click the green triangular play button at the bottom of the panel. If the "repeat" box is checked, the movie will keep playing until you press the stop button

Click the disk image with Save... to export your movie.

Time Sequence and Batch Movies

A Time Sequence movie can only be made if you loaded a set of volumes froma a directory that meet the time sequence convention. If you have a directory of 100 files, each labelled “image_T000.tif” through “image_T099.tif”, for example, you have a valid time sequence if your first volume to load is any 1 of the 100 files. VVDViewer will automatically check “Time Sequence / Batch” for you, set the start, end, and current times (based on the # of the file you loaded), and update the movie time slider to where this file is in the sequence.

A Batch Sequence movie plays a sequence of volumes stored in a single directory. For example, if you have “volumeA.tif”, “volumeB.tif”, and “volumeC.tif”, in a directory, and you load “volumeA.tif”, the movie playback will alternate between the three files.The volumes may or may not be related. The playback works exactly the same as with a time sequence. The number of frames equals up to the number of files in the directory in which your first loaded volume is located.

Movie Length is the length (in seconds) the exported movie will be.

Rewind When this box is checked, the movie will play forward then backwards

FPS (frames per second) determines how long each frame will be shown before advancing to the next frame

To view your movie, simply click the green triangular play button at the bottom of the panel. If the "repeat" box is checked, the movie will keep playing until you press the stop button

Click the disk image with Save... to export your movie.

Advanced Key Frame Movies

The Advanced tab of the Record/Export panel allows you to create movies in which the rendered 3D image transitions smoothly through a series of "key frames" that you define.

To create a Key Frame movie, first change how the volume appears in the Render View panel by adjusting one of the following:

• X, Y, and/or Z Rotation
• Translation (position in Render View window) • Scale (zoom)
• Cropping (using the Clipping Planes panel)
• Visibility (showing or hiding channels via Workspace panel) • Channel intermixing mode Layered, Depth, or Composite

Then, add the frame to the Key Frames table in Advanced tab of the Record/Export panel by clicking the Add button below the table.

Repeat as many times as desired. Then when you press the green triangular Play button, VVDViewer interpolate frames between the key frames during playback. Unfortunately, time and batch sequences are not available in combination with key frames.

The following information is included in the Key Frames table : ID: This is the ID number of the key frame. If you choose to, you may reorder key frames by dragging and dropping them anywhere in the list. The ID is generated starting at 1 and increases during the runtime of VVDViewer. The ID is usually the only way to decipher between the various key frames created, unless you add a “Description” (see below).
Frame: This indicates at which movie frame this particular key is active. You may reset the currently viewed key by double clicking on that key.
Inbetweens: This column indicates how many frames will be inserted between this key and the previous key. The first key in the list is always zero.
Interpolation: This can be either “Linear”, which means between the keys, frames are exactly 1/#inbetweens steps from one key to the next, or “Smooth”, which means the frames slowly ramp up to the transition, and slowly ramp down to the end of the key frame in an “S-curve” fashion. This can be changed by clicking on the “Linear” or “Smooth”, which opens a drop-down menu.
Description: You can click and add your own description for each frame to help you determine which key it is.

Options below the table include:
Default: This sets the default values that will be chosen for Inbetweens and Interpolation when new keys are added. Add: Adds a new key frame to the list with the current rendering transformations, cropping, and channel visibility as seen in the Render View panel.
Delete: Deletes the selected key frame.
Del. All: Deletes all of the key frames in the list.

FPS (frames per second) determines how long each frame will be shown before advancing to the next frame. Note that because you enter the number of frames between each key frame, there is no option to select movie length. Only a FPS is necessary. You can determine the movie time by dividing the total number of frames in the table by the current FPS. For example, if you have 90 frames, and your FPS is 30, the movie will be 3 seconds long.

Automatic Key Generation

The Auto Key tab allows you to select an automatic key generation scheme from a list, and then generate key frame animations. You first choose an auto key type, then click “Generate”. Or, you can double-click an option. This brings you to the “Advanced” panel, which contains automatically generated keys. You can then interact with the automatically generated keys using the same controls provided in the “Advanced” panel. Currently, we provide three options for automatic key generation. These three options are:
Channel Combination nC1. It sets a key for each isolated channel within a multi-channel data set. You can browse each channel individually with this setting.
Channel Combination nC2. It sets a key for each two-channel pair within a multi-channel data set. You can use this function to visualize colocalization regions between any two-channel combinations.
Channel Combination nC3. Similar to nC2, it sets a key for each triple-channel combination. You can use this setting to visualize all colocalization cases of three channels.

Frame Cropping

Often, the important data do not cover the entire render view panel. Recording the whole frame, including a lot of empty space, will make a movie file larger than necessary. The Cropping tab allows you to crop what is captured in the rendering frame to a smaller area.

When "Enable cropping" is selected, a yellow rectangle appears in the Render View panel indicating the pixels that will be used in the movie file. The yellow rectangle is set automatically, based on the area that is covered by data.

The “Center X” and “Y” fields allow you to modify where the center of the movie will be in pixel coordinates. In addition, you can modify the “Width” and “Height”. The yellow box will not be in the output, but will remain visible if “Enable Cropping” is selected. The “Reset” button allows you to recalculate the cropping region if you have rotated, zoomed, or panned the view. The cropping square does not resize with the program interface window as you resize it on your computer, but you can click “Reset” to get the snug cropping region back in the render view.