Vesselucida 360 interface

The Vesselucida 360 user interface has two principal windows:

2D window: Includes the File menu and tool ribbons with tools for optimizing images, conducting batch processes, defining regions of interest, and setting software preferences.
3D environment: Tools for tracing/detecting structures to model your images, segmenting large/complex images to facilitate tracing, and capturing movies to present your work to others. Learn more about the 3D environment here.

2D window and 3D Environment

When you open Vesselucida 360 software, both the 3D Environment and 2D windows will open.

You can dock the 3D window or close it (with the "X" in the upper right corner), but closing the 2D window will shut down Vesselucida 360 software.

Light and Dark interface themes

Go to File > Preferences > Display and choose the Light or Dark theme for the Vesselucida 360 software interface.

We created the Dark theme for working with fluorescence images

and recommend the Light theme for brightfield images.

Tool Ribbons in the 2D window

Tools for working in the 2D window are grouped by tasks. Some "buttons" appear on more than one ribbon to help facilitate your work.
Tools are clustered into groups on each ribbon. Press the gear icon to go right to Preferences that affect the tool group.
You can hide the ribbons to expand your working space by right-clicking the ribbon area and choosing Minimize the ribbon

The Workspace ribbon includes all of the dockable windows.

The publish ribbon includes tools for sharing your work with others, such as adding a scalebar, and exporting images of your tracings in image or vector formats.

The Image ribbon includes tools for adjusting and organizing images, and many other functions.

Quick access tools

The top of the 2D window includes tools to help speed up your work.

Quick Access bar The Quick Access bar contains the most frequently used tools. Add any tool in the 2D window to the Quick Access toolbar by right clicking on it and choosing Add to Quick Access Toolbar	Quick Launch/Tool search If you can't find a tool, but know its name, type it into the Quick Launch box on the right. Vesselucida 360 software searches for the tool and displays choices. Just click a choice to go to that tool.

Drag and drop files to open them

The easiest and quickest way to get started with Vesselucida 360 software is to simply drag and drop files onto the application window. You'll see one of two windows open next, depending on whether you drop image or data files. Either way, these dialog boxes enable you to indicate how you want Vesselucida 360 to handle your files.

Image and image-containing files

for example Leica .lif or Zeiss .czi files

the Image Opener window appears:

Data files

for example MBF Bioscience .dat files

the Drag and Drop File Open window appears:

3D Environment

If it's not already open, click the 3D environment button on either the Image or Workspace ribbon to open the 3D environment.

Navigating in the 3D environment

Use your mouse and the navigation tools in the 3D button bar

Use your mouse to:

Load images by dragging and dropping them onto the Vesselucida 360 window. The Image Opener and/or the Image Scaling dialogs will prompt you for information about the files if needed.
Rotate: Drag the mouse to rotate the image around a pivot point.
Zoom: Scroll the mouse wheel to zoom in or out.
Pan: Hold the Shift key on your keyboard and drag your mouse to pan.

The 3D environment button bar includes many commonly used functions (some are repeated from the 2D window).

Customize image and scene display

Learn more about Image mode

Learn more about changing the Scene display

Vessel tracing and detection

There are three tracing methods and you can easily switch between methods while tracing.

For complex structures, start with Automatic then switch to User-guided to complete the tracings. You may also use the Smart manual method. Don't forget to check Partial Projection in the Image panel before you start tracing.

Editing Vessels

Use the Edit Vessels panel to edit, connect, detach, classify segments, and to visualize flow direction (also see Editing vessels in 2D).

Puncta detection and editing

Learn more about puncta detection and editing.

Contour drawing and editing in the 3D environment

Contours are 2-dimensional shapes that can be drawn in either the 2D window or in the 3D environment to define regions of interest.

Marker placement and editing

Place markers in either the 2D window or in the 3D environment (shown in 3D below)

Additional tools in the 3D environment

In addition to buttons for tracing and image modes in the 3D environment are an additional set of tools for working with your images.

	Change Scene Display: Click the button to modify display settings, such as adding scale bars, 3D-stereo effects, and background colors.
	Create Movies: Create mp4 movies of your images or tracings.
	3D Settings: Save your settings for automatic detection and tracing of structures.
	The Edit button appears when editing functions are available. For example to edit somas, trees, spines, markers, or contours.
	Subvolume: Specify subvolumes (regions of interest) and load image data only from those regions. You can then work in easily managed portions of the image volume. By creating subvolumes that overlap slightly, you can reconstruct the entire image volume piece by piece.