Users
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| − | General | + | == List of BioImageXD features == |
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| + | '''General''' | ||
* Open source code | * Open source code | ||
* Free | * Free | ||
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* Extendable program architecture, supports selected libraries (VTK, ITK) | * Extendable program architecture, supports selected libraries (VTK, ITK) | ||
| − | Graphical user interface | + | '''Graphical user interface''' |
* Single large window with re-sizeable panes/parts that are also switchable visible/invisible | * 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 | * Main panes/parts: main tool bar, file tree, view panel (maximizable), dataset info, task panel | ||
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* Short explanation texts always on screen for most features | * Short explanation texts always on screen for most features | ||
| − | File input/output features | + | '''File input/output features''' |
* Internal file tree (switchable visible/invisible, contents savable for next program start) | * Internal file tree (switchable visible/invisible, contents savable for next program start) | ||
* Open dataset (supports 10 common bioimaging file formats) | * Open dataset (supports 10 common bioimaging file formats) | ||
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* Open/save 3D view scene | * Open/save 3D view scene | ||
* Import/export images (supports 5 common image file formats) | * Import/export images (supports 5 common image file formats) | ||
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| + | '''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) | ||
Revision as of 07:55, 5 July 2012
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)
