Users

Video links

• 3D rendering. Illustrates how multi-channel 3D renderings can be created, changed, adjusted and interacted with.
• Animation. Illustrates how a camera path animation is created, all the way to the finished video file product.
• Segmentation. Illustrates how a procedure list for segmentation is set up and used to analyze receptor clusters on cell surface.

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

Visualization modes

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)

Tasks

Adjust task

• Graphical intensity transfer function, adjustable timepointwise
• Controllers for brightness, contrast, gamma, min/max values & thresholds, smooth start/end 
• Interpolation with up to 5 specifiable timepoints, for bleaching correction etc.

Merge task

• Combines gray scale datasets into an RGB color image (which can subsequently be volume rendered in 3D mode)
• Each channel adjustable with graphical intensity transfer function (same as in Adjust task)
• Alpha channel construction method selectable (3 options)

Colocalization task

• Analyzes and visualizes colocalization between two channels
• Both manual and automatic threshold determination
• 2D histogram (savable as image)
• 3 methods for P-value calculation
• Calculates approximately 40 colocalization parameters (savable as CSV file)

Procedure list task

• Creates command pipelines (savable as presets) from approximately 90 different available procedures (each fully adjustable by clicking them)
• To help assembling procedure lists, each procedure has on-screen explanation text with acceptable inputs and outputs
• Outputs both images and analysis results (latter exportable as CSV files)
• Noise removal (Gaussian smooth, Gradient anisotropic diffusion, Median, Anisotropic diffusion, Hybrid median 2D, Mean)
• Iterative deconvolution and PSF generation
• Feature detection (Gradient magnitude, Find local maxima, Sobel, Difference of Gaussians, Canny edge detection, Sobel edge detection, City block distance, Danielsson distance map, Euclidean distance)
• Morphological operations (Dilate, Erode, Variance, Range, Binary thinning, Grayscale fill hole)
• Fourier transforms and filters (FFT, Inverse FFT, Butterworth low pass, Butterworth high pass, Ideal low pass, Ideal high pass)
• Non-uniform illumination correction and Sigmoid filter
• Image arithmetics (Subtract, Add, Divide, Multiply, Sin, Cos, Exp, Log, Sqrt, Invert, Shift and scale)
• Logical operations (And, Or, Xor, Not, Nor, Nand)
• Automatic background subtraction (3 methods)
• Thresholding (Threshold for maximum object number, Otsu threshold, Otsu multiple thresholds, Dynamic threshold, Threshold)
• Morphological watershed segmentation
• Region growing (Confidence connected threshold, Connected threshold, Neighborhood connected threshold)
• Active contours
• Segmented object processing (Re-label image, Connected component labeling, Object separation, Filter objects)
• Segmentation-based analyses (Analyze polydata, Analyze motion tracks, Analyze segmented objects), calculate in total approx. 70 parameters
• Voxel-based analyses (FRAP analysis, Timepoint correlation, Analyze region of interest), calculate in total approx. 20 parameters
• Colocalization analyses (Calculate thresholds for colocalization, Analyze colocalization, Object colocalization), calculate in total approx. 55 parameters
• Region of interest processing (Extract a subset, Subtract ROI, Use ROI mask)
• Simulations (4D particle simulations)
• Registration (Translation registration, Versor rigid registration, Rigid registration 2D, Deformable registration, Translation registration 2D, Multi resolution translation registration, Slices translation registration 2D)
• Tracking (Create motion tracks, Visualize motion tracks 2D)
• Dataset conversions (Combine time series, Convert data type, Convert to polygonal data, Combine images, Extract components, Combine different intensity range images)

Batch Processor

• Processes all selected datatsets, outputs both images and analysis results
• Supports multiple procedure lists (either channel specific or for all channels)
• Aggregates selected results (of approximately 120 available parameters) into spreadsheet format (CSV file)
• Presets from Procedure list task available
• Analysis settings can be saved/opened

Animator

• Creates movies of the scene rendered in 3D mode
• Adjustable frame size, frame rate and duration
• Two combinable animation techniques: keyframe and camera path (can be set to share a frame for smooth transition between techniques)
• Animation movements adjusted in 3D preview window
• Camera path features: free motion path, circular paths and movement pause
• Video-editor type interface based 3 types of tracks (timepoint changes, keyframes, camera path nodes)
• Tracks items can be resized and moved individually or in batches from menus
• Output as series of still images (5 formats) and/or videos (8 formats) with adjustable quality

Other

• Preferences dialogue (for setting up default paths, performance options, automatic resampling etc.)
• View panel updating switchable on/off/automatic
• Editor for look-up-tables (palettes) with freehand/node editing of RGB color transfer function and saving/opening of palettes
• Resize dataset (in X/Y/Z; one button switching original/resized)
• Convert dataset to 8-bit (with adjustable mapping of values)
• Previous path locations are remembered
• Mouse tooltips
• Getting Started Guide (viewable from software)
• Automatic bug reporting feature (activates after program crash)
• Manual bug reporting feature (activatable by user at any time)