Users

List of BioImageXD features

General

• Open source code
• Free
• Supports both 32-bit and 64-bit operating systems: Win, Mac OSX, Linux
• Single installable package
• 3D timelapse support in all functionality
• Features extensively adjustable
• Image data read only on demand (not upon file loading)
• Extendable program architecture, supports selected libraries (VTK, ITK)

Graphical user interface

• Single large window with re-sizeable panes/parts that are also switchable visible/invisible
• Main panes/parts: main tool bar, file tree, view panel (maximizable), dataset info, task panel
• Other panes/parts: view panel top toolbar, view panel side toolbar, view panel configuration, histograms, Python shell
• Color coding (expert features & settings are colored red)
• Short explanation texts always on screen for most features

File input/output features

• Internal file tree (switchable visible/invisible, contents savable for next program start)
• Open dataset (supports 10 common bioimaging file formats)
• Save dataset (supports BioImageXD file format; timepoints selectable upon saving)
• Open/save settings
• Save snapshot image (supports 3 common image file formats)
• Open/save 3D view scene
• Import/export images (supports 5 common image file formats)

View panel features

• Operates in any of 5 visualization modes: Slices, Gallery, Orthogonal, Projection, 3D
• Sliders for choosing timepoints/z-slices when applicable
• Zoom in/out/to fit/to user-selected region
• View angle/axis selection/rotation buttons (in 3D mode)
• Changeable interaction modes (trackball/joystick/camera/actor) (in 3D mode)
• Interpolation method adjustable (4 options)
• Displays current/original dataset dimensions
• Hold-down button for switching between original/processed dataset
• Button for switching between resized/original dataset
• Eyedropper tool for retrieving pixel/voxel information
• Regions of interest (ROIs) can be drawn with 3 tools: circle, rectangle, polygon
• Scalebar drawing
• Annotations (such as ROIs) can be deleted, moved, resized and their color changed
• Convert ROI to mask / mask selection

Slices visualization mode

• Displays chosen slice

Gallery visualization mode

• Displays all slices of chosen timepoint or all timepoints of chosen slice as small images

Orthogonal visualization mode

• Displays orthogonal sections (positions selectable) through the dataset along the three spatial axes (X, Y, Z)

Projection visualization mode

• Displays either a maximum intensity projection or an average intensity projection

3D visualization mode

• Displays 3D renderings interactively, can be rotated, panned and zoomed with mouse
• General settings for lighting, background color and view angle
• 3D mode settings can be saved/opened
• Renderings are created by 11 different modules that can be loaded/unloaded and switched on/off
• Several rendering modules can be combined, each rendering also different data channels
• Angle measurement module (for measuring/drawing angles in 3D with mouse)
• Axes module (draws X/Y/Z axes, with adjustable lengths)
• Clipping box module (clips all or selected modules inside/outside defined box)
• Clipping plane module (clips all or selected modules on one side of defined plane)
• Distance measurement module (for measuring/drawing distances in 3D with mouse)
• Orthogonal slices module (displays adjustable orthogonal slices along all three spatial axes)
• Surface rendering module (creates one or several surfaces at selectable iso-values, adjustable surface transparency and intensity, 4 different surface rendering methods, several smoothing and simplifying options)
• Visualize protein databank file module (input selection for PDB file to visualize, adjustable tube & sphere radii)
• Visualize motion tracks module (input selection for tracks file to visualize, tracks can be individually chosen from a list and visualized with same/actual starting points, minimum track length specifiable, adjustable tube & sphere radii)
• Volume rendering module (graphical color and opacity transfer function editor (RGBA) with feehand/node adjustment and opening/saving of look-up-tables, 4 different volume rendering methods, adjustable interpolation and rendering quality, shading)
• Warp scalar module (displays 2D slice as 3D map, selectable slice, adjustable scale factor and adjustable surface smoothing)