GUI Overview

Essential aspects of the interface

The following image shows the main elements of the graphical user interface (GUI). For more detailed documentation on the various elements of the interface, click on the green or blue areas of the image.

The interface of the default DICOM workspace consists mainly of 2 parts:

1. The DICOM Explorer on the left (in blue). It allows you to import and export data, as well as select the series to be visualized.
2. Depending on the data imported, different viewer/player types (represented by a tab) are displayed in the main section (green). Menus , toolbars and tools change according to the type of viewer selected.
   • The selected viewer is the image above is the DICOM 2D viewer which is the viewer opened by default.
   • A tab containing a multi-view layout can display images from only one patient. However, one patient can appear in several tabs.
   • A tab is also docked panel that can be arranged by dragging and dropping it to the desired location. This makes it possible to display 2 tabs side by side.
   • See also DICOM Explorer to understand how to navigate through the Patient/Study/Series/Image.

List of other viewers/Players in the DICOM workspace

• Multiplanar Reconstruction (MPR) viewer
• Maximum Intensity Projection (MIP) viewer
• DICOM 3D viewer
• DICOM ECG viewer
• DICOM Structured Report (SR) viewer
• DICOM Audio player
• DICOM PDF viewer (default system application associated with pdf files). Same for other encapsulated documents.
• DICOM Video player (default system player associated with mpg files)

List of other workspaces

• Dicomizer
• Explorer of standard images (based on the non-dicom-explorer.json configuration profile)

DICOM Import

How to import DICOM files

Weasis can open DICOM files from various ways and sources: drag and drop, local device, DICOM ZIP, DICOM CD/DVD, DICOM Query/Retrieve, and from commands locally or remotely.

From the system file explorer

Drag and drop

Files or folders selected from the system file explorer can be opened by dragging and dropping into the central area of Weasis.

• Empty central panel: Any files than ca be open by one of the viewers (e.g. standard images such as TIFF, PNG, JPEG…)
• DICOM Explorer and DICOM viewers (SR, AU, MPR, 2D and 3D) in the central panel: Only DICOM files. Opens the default viewer according to the files.

File association

Dicom files can be opened by double-clicking them from the system file explorer.

From Weasis menu or toolbar

From the main menu, open File > Import > DICOM or from the first import button in the toolbar.

In order to import DICOM CD/DVD go the main menu, open File > Import > DICOM CD or from the second import button in the toolbar.

Local Device

• Files and/or folders: list of selected items or unique path
• Search recursively: when this option is activated the import takes into account the subdirectories
• Open in new tab: behavior to automatically open the images of a patient when loading DICOM files

DICOM ZIP

• Select: browse a DICOM zip file. When the archive file is encrypted, a password prompt is displayed.
• Open in new tab: behavior to automatically open the images of a patient when loading DICOM files

DICOMDIR

It may be from a DICOM CD/DVD or a folder containing a DICOMDIR

• Path: browse a folder containing a DICOMDIR
• Detect CD-ROM: try to load a DICOM CD/DVD
• Copy images into the local temporary directory: useful for slow reading device like CD-ROM

DICOM Query/Retrieve

• On DICOM Source tab:
  • Archive: select the archive to query
    • With DICOM nodes: classic DIMSE C-Find with C-Move, C-Get or WADO-URI for retrieving DICOM files
    • With DICOMWeb nodes: QIDO and WADO-RS for retrieving DICOM files (no other options are required)
  • Retrieve (only with DICOM archive): the protocol to retrieve the images
    • C-MOVE: the classic DIMSE protocol (accepts all sop classes, not recommended for WEB)
    • C-GET: transfer syntaxes are negotiated by each sop classes according to a configuration file
    • WADO-URI: required a WADO server (C-Find + WADO retrieve)
  • Calling Node (only with DICOM archive): select the adapted calling DICOM node
  • More options: allows you to open the preferences to configure the DICOM nodes
• On Search Criteria tab:
  
  1. Select a pre-registered item (bottom right of the Search Criteria panel) or Fill the search criteria. Criteria can be saved and reuse later, since Version4.1.0 the item selected in the combo box is automatically applied the next time this window is opened (the default value is Empty).
  2. Adjust the limit to the maximum number of exams in the response. Set the limit to 0 to avoid this constraint. For DICOMWeb the limit is the number of elements on a page, and you can go to the next page with the spinner buttons.
  3. Click on Search
  4. Select the exams you want to import
  5. Start importing and close the window

From commands

See this page

DICOMWeb Import

How to configure DICOMWeb node

This page explains how to configure a remote archive in DICOMWeb and then use this DICOMWeb node to retrieve exams remotely. However, it is also possible, without any prior configuration, to launch Weasis from a web context by passing it some parameters to retrieve images in DICOMWeb.

From the main menu, open File > Preferences (Alt + P) and select DICOM node list.

Google Cloud Healthcare API

Google provides a Cloud Healthcare API’s implementation of DICOMweb.

1. Add a new DICOMWeb node and enter a description
2. Select DICOMWeb service
3. Enter the URL of a Google repository (must ends with /dicomWeb)
4. Add an authentication by clicking on the Manager button and then click on Add

1. Select the Google Cloud Healthcare template
2. Click on Fill and optionally edit the name
3. Enter your Client ID and Client Secret, Click on OK and close the other windows. Then open the DICOM Import dialog and select the node.

Currently, the DICOMWeb service for getting thumbnails doesn’t work in the Google API.

Orthanc WEB Server

Orthanc is a lightweight DICOM server with DICOMWeb capabilities.

Currently, the DICOMWeb service of Orthanc doesn’t support the thumbnail service.

Create a new DICOMWeb node with the following URL (example with the demo server without authentication):

https://demo.orthanc-server.com/dicom-web

dcm4chee-arc-light

Kheops

DICOM Export

How to export DICOM files

Exporting the selected view

From the toolbar icon or from the main menu File > Export > Exporting view export the selected view either to the clipboard or to image file (PNG, TIF, JPG, JPEG2000).

Current view

Export the view as it is (size and overlay).

Anonymize: It allows you to remove identifying information in overlay.

Original Image

Export the view according to the original image with some options.

• Size: Change the image size in percent
• Preserve 16-bit per channel: Option to preserve the pixel depth (e.g. 16-bit in PNG/JPEG 2000/TIFF, double values in TIFF). When this option is applied, the pixel values will match with the Modality LUT values (e.g. Hounsfield values). Exporting in JPEG Lossy is only possible when unchecked for 8-bit image.
• DICOM Pixel Padding: Apply the DICOM pixel padding when checked
• DICOM Shutter: Apply the DICOM shutters when checked
• DICOM Overlay: Apply the DICOM overlays when checked

DICOM Export

In order to open the DICOM export window click on toolbar icon or from the main menu File > Export > DICOM

Local Device

1. Select Local Device item
2. Choose the exporting options
   • Transcoding: It allows you to change the DICOM transfer syntax. Use this option only if you understand well what you are doing.
   • Generate new unique identifiers: Create new UIDs for some attributes. Within an export, the consistency between all the UIDs and their references is preserved.
   • Include DICOMDIR: Create DICOMDIR file
   • DICOM CD folders: Add a directory to be compliant with DICOM CD
   • Keep directory names: Preserve the name in the directory hierarchy (not compliant with DICOMDIR)
3. Select the patient/study/series/instance to export. Note: series created by Weasis have a flag “NEW”
4. Export the selection and close the Window

DICOM Send

1. Select DICOM Send item
2. Select the destination node (either a DICOM node or a DICOMWeb node)
3. Select the patient/study/series/instance to export. Note: series created by Weasis have a flag “NEW”
4. Send the selection to the destination and close the Window

CD/DVD Image

1. Select the CD/DVD Image item
2. Choose the exporting options
   • Transcoding: It allows you to change the DICOM transfer syntax. Use this option only if you understand well what you are doing.
   • Generate new unique identifiers: Create new UIDs for some attributes. For an export, the consistency between UIDs and their references is preserved.
3. Add JPEG images allows extracting the images and the encapsulated files (video, audio and PDF) into a JPEG folder
4. Add Weasis allows embedding the viewer into the iso image. This option is only possible on Windows x86-64 (for exporting and running). Running the viewer directly on a CD/DVD ca be quite slow. To avoid that you can install the ISO on a USB stick or read the CD with a locally installed viewer as described in README.html.
5. Select the patient/study/series/instance to export
6. Export the selection and close the Window

DICOM Explorer

Structure and display of Patients/Studies/Series

DICOM Explorer

The DICOM Explorer is the panel on the left that displays the Patient/Study/Series representation defined in the DICOM standard.

The data displayed in the DICOM Explorer can be imported form different ways.

Patient Level

• Weasis allows multi-patient display. By default, when images are imported a tab with the patient’s name opens in the main area.
• A tab containing a multi-view layout can only display images from a single patient.
• Changing patients can be done either through the first combobox in the DICOM Explorer (see image above) or by selecting a tab in the main area.
• In the combobox the patients are sorted in alphabetical order regardless of case and according to the regional setting.
• Studies and Series are displayed within the same patient when the metadata Patient Name and Patient ID are the same. Otherwise, new patients are displayed.

Study Level

• A study contains one or more series (thumbnails) belonging to a patient. A line representing the study surrounds its series (see image above).
• By default, the studies are sorted by reverse chronology order (since Version4.1.0 “Study data sorting” can be changed in the menu “File > Preferences > DICOM > DICOM Explorer”). If there is no study date then the studies are sorted alphabetically according to the Study Description.
• By default, all the studies are displayed, however you can choose to display only one of them from the study combobox.

Series Level

• A series is represented by a thumbnail that contains a certain number of images (number displayed at the bottom left).
• According to predefined rules, some series are separated into sub-series also represented by a thumbnail with a number preceded by ‘#’ in the upper right corner. Series splitting is necessary for the consistency of some tools such as the MPR, cross-lines and synchronization of series. However, sometimes separation is not desired, and sub-series can be re-merged using the context menu.
• The sorting of the series is done by the serial number and if this last one is not present then in a chronological way by the date of the series or other dates.
• To open new series:
  • Drag and drop a thumbnail in the main area (if the series is dropped in a view of the same patient then the series is replaced otherwise a new tab is created).
  • Double click or navigate with the up/down arrow key and press return on a selected thumbnail (if a view of the same patient exists then the series in the view surrounded by an orange line is replaced)
  • Select one or more thumbnails and choose an action from the “2D DICOM Viewer” context menu:
    • Open: Opens the series in the most appropriate layout (replaces the series if the patient’s tab already exists)
    • Open in new tab: Opens the series in the most appropriate layout in a new tab.
    • Open in screen: Opens the series in the most appropriate layout in a specific screen.
    • Add: Adds the series to the current patient’s layout if exists.

Preferences

From the main menu “File > Preferences > DICOM > DICOM Explorer”:

• Thumbnail size: defines the width of the thumbnails and adjusts the panel accordingly (Default: 144). It is recommended to restart the application after this change.
• Study data sorting: allows sorting the studies by chronological order or inversely chronological (Default: reverse chronology order). Since Version4.1.0.
• Open in new tab: behavior to automatically open the images of a patient when using WADO or WADO-RS (Default: All the patients)
• Download all series immediately: allows starting the download of the series immediately when using WADO or WADO-RS (Default: true). If unchecked then you must click on the play button on each series or globally at the bottom of the thumbnail list.

DICOM 2D Viewer

Displaying DICOM images

The 2D viewer is the default viewer when opening a DICOM series containing images.

Open the 2D viewer

The 2D view can be opened with in the toolbar or by right-clicking on the thumbnail in the DICOM explorer.

The rulers K show a real size when it can be calculated from the DICOM file. When a text M above the calibration is displayed, it gives information about the calibration type. Here are some examples:

• At dector: The calibration of the projection radiographic image is done at the detector level
• Magnified: The calibration of the projection radiographic image is corrected using the magnification factor (e.g. mammography, see the image above)
• Used fiducials: The calibration is based on fiducials (e.g. manual calibration with a ruler in the image)
• At scanner: The calibration comes from a media which has been digitized (e.g. film digitizer)

Toolbars A

Viewer Main Bar

Select the preferred actions for the three mouse buttons and the mouse wheel:

• Mouse left button: The default value is Window/Level. Action can also be changed from the context menu F and the key shortcuts.
• Mouse right button: The default value is Context Menu
• Mouse wheel: The default value is Series Scroll
• Mouse middle button: The default value is Pan

Where the possible actions are:

• Pan: Move the image position. T key to select the action. Alt + Arrows keys to pan when another action is selected.
• Window/Level: Change the contrast of the image. W key to select the action.
• Series Scroll: Scroll through the images of the current series. S key to select the action.
• Zoom: Zoom in/out the image. Z key to select the action.
• Rotation: Rotate the image with a free angle. R key to select the action.
• Measure: Draw a graphic for measuring something. M key to select the action.
• Draw: Draw a graphic for annotating. G key to select the action.
• Context Menu: Display the context menu. Q key to select the action.
• Crosshair: 3D cursor. H key to select the action. Ctrl + click or Ctrl + Shift + click allows changing Window/Level.
• No Action: Do nothing. N key to select the action.

• Default layout: Change the layout of the view. DICOM Information and Histogram are specific layouts where information is automatically updated when scrolling through the series.
• Synchronize: The synchronization feature lets you apply the same settings to other images.
  • None: No synchronization is applied between series.
  • Default Stack: When selected, the layout is synchronized (window/level, scrolling, zoom) only with the series sharing the same Frame of Reference UID (0020,0052). This is the default behavior.
  • Default Tile: When selected, the layout is applied in tiled mode (image mosaic of the current series) and is synchronized (window/level, scrolling, zoom) with the image of the same series.
• Reset: Reset the image rendering (see below). Escape key to select the action.

Toolbars available in the DICOM 2D viewer

• DICOM Import
• DICOM Export
• Screenshot
• Viewer Main Bar (see above)
• Measurement
• Zoom
• Rotation: Rotate the image by 90° clockwise or flip it horizontally. Note visible by default.
• DICOM Header
• Lookup Table
• Basic 3D: MPR and MIP (disabled if the series has less than 5 images)
• 3D Viewer (disabled if the series has less than 5 images)
• Cine
• Key Object Selection

Viewer’s tools

Here is a list of the tools which are associated to the DICOM 2D viewer.

The mini-tool is always visible and the other tools are displayed by clicking on the vertical button. The normalize button allows you to insert the panel into the main layout. Otherwise, the panel is displayed as a popup window with the pin option (which is not recommended, as it hides other panels).

Mini-tool B

Allows you by default to scroll through the images of the selected series (surrounded by an orange line). From the combobox at the top, the mini-tool can also be configured to change the zoom or the rotation of the image.

Display C

It lets you control the display of the image and the graphic objects.

The Apply to all views option allows you to apply the same display settings to all the views within the selected tab. If unchecked, the display settings are only applied to the selected view (surrounded by an orange line).

Image

Display options for the image. Unchecking the Image option will hide the image and display only the annotations and the graphic objects. The other options are related to DICOM specifications:

• Dicom Image Overlay: Apply the DICOM overlays when checked. The overlay color can be changed.
• Shutter: Apply the DICOM shutters when checked
• Pixel Padding: Apply the DICOM pixel padding when checked

Dicom Annotations

Display transformation properties and DICOM information on the image.

• Annotations: Display DICOM information on the image corners:
  • G The top left: Patient information
  • H The top right: Study information
  • I The bottom right: Series information (related to the modality type)
  • J The bottom left: Image information and its position in the series
• Minimal Annotations: Reduce the number of annotations. Use space or i key to toggle between the 3 states (minimal, none, all).
• Anonymize: Hide identifying information only in the views not in other places of the GUI like the tab title. Must be used with the screenshot tool when exporting image.
• Scale: Display the rulers on the left and the bottom of the image K
• Lookup Table: Display the LUT on the image
• Orientation: Display the orientation of the image N
• Window/Level: Display the window and level values J
• Zoom: Display the zoom value J
• Rotation: Display the rotation value J
• Frame Value: Display the frame number J
• Pixel (Value/Position): Display the pixel value and the position of the cursor J

Drawings

Check/uncheck to show/hide the graphic objects (see Draw & Measure).

Image Tools D

Image Tools contains all the tools to modify the image rendering.

Windowing and Rendering

Transform

Allows you to zoom, rotate and flip the image. Zoom and rotation can also be configured with the mini-tool or the mouse actions.

Cine

The Cine start button lets you scroll through the images in a series at a certain speed (frame per second). The speed values comes from the DICOM file if exists. The cine options can also be changed from the context menu.

• Click on Cine stop button to end the animation.
• Click on Loop Sweep toggle button to change the cine mode: looping vs sweeping.

Reset

It allows you to return to the default image rendering for all or specific parameters. Also available from the toolbar button or from the context menu.

Draw & Measure E

Other specific tools

• DICOM RT tools (for radiotherapy studies)
• DICOM Segmentation tools (not yet available)

Preferences

From the menu “File > Preferences > Viewer > “2D Viewer”:

Mouse Action Sensitivity

The sensitivity of the mouse drag can be changed according to your preferences for the following actions: Window, Level, Zoom, Rotation and Series Scroll.

Zoom

Zoom interpolation is the process of creating new pixels between existing pixels in an image when it is zoomed in or out.

• The Nearest neighbor interpolation is the simplest method. Basically, it extends the pixel value.
• The Bilinear method averages the values of the four nearest existing pixels to the new pixel. This produces slightly sharper results than nearest-neighbor interpolation, but it is also slightly slower.
• The Bicubic method is similar to bilinear interpolation, but it uses a 16-point kernel instead of a 4-point kernel. This produces even sharper results than bilinear interpolation, but it is also the slowest method.
• The Lanczos method uses a sinc kernel to resample the image producing the sharpest results. It is moderately fast, between bilinear and bicubic.

The default value is Bilinear. The Nearest neighbor interpolation is faster but produces aliasing artifacts.

Other

• Apply Window/Level on color images: When checked, the window/level is applied on the RGB channels of the image. Otherwise, the window/level has no effect when unchecked.
• Inverse level direction: When checked, the level direction with mouse actions is inverted (dragging down will increase the brightness) according to the Basic Image Review profile. Otherwise, dragging down will decrease the brightness when unchecked.
• Apply by default the most recent Presentation State: When checked, the most recent Presentation State Object is applied on the related image. Otherwise, it is required to select it from .
• Overlay color: change the color and the opacity of DICOM overlay. The default color is white. The opacity can be changed from the transparency or alpha slider of the different color models in the color picker.

MPR Viewer and 3D cursor

MPR Viewer and 3D cursor (crosshair)

Orthogonal multiplanar reconstruction (MPR)

The orthogonal multiplanar reconstruction (MPR) allows you to create, from the original plane (usually axial), images in the two other planes of the Euclidean space. Only planes along the 3 axes (x,y,z) can be displayed, an oblique plane cannot be obtained with this tool.

The MPR view inherits most of the DICOM 2D viewer properties. It can be opened with in the toolbar or by right-clicking on the thumbnail in the DICOM explorer.

When the tab containing the MPR views is selected, the crosshair tool is automatically applied on the left mouse button. Note that it is possible to change the window/level with the ctrl key while keeping crosshair selected.

By default, zoom and window/level are synchronized between the 3 views. The MRR views can be displayed in different layouts .

Try to load a volume dataset and open the MPR viewer. Launch

3D cursor (crosshair)

The 3D cursor allows you to synchronize the position of several views sharing the same 3D coordinate system.

In order to know which series sharing the same coordinate system, you can select more than one series from the DICOM explorer by right-clicking on a series and selecting “Select related Series”. Then open the series selection by right-clicking again and selecting “2D Viewer > Open”

The crosshair tool can be selected in the mouse buttons on the toolbar or by right-clicking on a view.

Try to load several series and select the 3D cursor. Launch

Preferences

From the main menu “File > Preferences > Viewer > MPR” (Since Version4.1.0):

• Auto center axes: Allows you to choose a behavior to recenter the cursor in the different views. The position can be returned to the center systematically with the “Always” option (see the image above) or with the 2nd option only when the position is almost no longer visible (the default value).
• Crosshair gap at the center: Defines the size of the empty space in the center of the crosshair
• Default layout: The preferred layout used when opening the MPR viewer

MIP Viewer

Maximum Intensity Projection (MIP)

The MIP viewer is a simple 3D viewer that allows to display the maximum intensity projection of a volume defined by a number of slice of the image stack.

The MIP viewer is also available in the 3D viewer with more advanced options of the volume rendering, but some minimal hardware requirements is necessary.

Open the MIP viewer

The MIP viewer can be opened with in the Basic 3D toolbar of the DICOM 2D viewer.

The MIP Options

This dialog is a modal window that allows you to change the MIP settings and build a new MIP series.

Try to load a volume dataset and open the MIP viewer. Launch

Projection type

The projection type defines the way the MIP is calculated. The options are:

• Min: Minimum Intensity Projection
• Mean: Mean Intensity Projection
• Max: Maximum Intensity Projection (the default value)

Slice position

The slice position is used to move around the series to apply the projection and display the result. The Image value represents the position in the series stack.

Slice thickness

The Image Extension value represents the number of slices to use for the MIP calculation. If the images are calibrated and contains the 3D position, the thickness is also displayed in millimeters.

Rebuild Series

It allows you to build a new MIP series according to the MIP options. In this new series the slice position and thickness are modified.

The new MIP series is added to the DICOM explorer and can be exported.

DICOM 3D Viewer

Displaying volume data

Since Weasis Version4.1.0 the 3D viewer allows displaying volumetric renderings with different options for adjusting the pseudo colors, the transparency, the shadows and the lighting according to the type of exam.

The volume rendering uses a ray casting algorithm and the OpenGL Shading Language (GLSL). Shader programming is used to create the necessary algorithms and data structures required for the ray casting computations to be executed efficiently on the graphics card. Therefore, minimal graphic resources are required.

Requirements

Some requirements related to the specifications of your graphic card are mandatory. They can be displayed in “OpenGL Support” from the menu “File > Preferences > Viewer > 3D Viewer”:

• Driver version: The OpenGL version must be at least 4.3 to support the Compute Shader (not supported currently on macOS)
• Max 3D texture dimension length: The limit of any dimension (X,Y,Z) of the volume data
• If you have other information in red, it means that the configuration is not optimal but in most cases can work (see how to limit the size of 3D textures)

Open the 3D viewer

The 3D view can be opened with in the toolbar or by right-clicking on the thumbnail in the DICOM explorer.

Try to load a volume dataset (Medical Demos from data.kitware.com) Launch

Toolbar A

Actions in the toolbar are:

• Allows you to fully reload the volume
• The orthographic projection maintains parallel lines unlike the perspective projection that provides a perception of depth. The default mode is the perspective projection.
• Opens the 3D preferences

For other buttons see below.

3D Rendering Tools

This tab contains all the tools to modify the volume rendering. If you want to return to the original settings, just click on the toolbar button or from the context menu.

Windowing and Rendering B

Some of the options described below are also available in the toolbar and in the contextual menus.

• Window: The width of a range of voxels values mapped to a specific range of display values.
• Level: The center of the range defined by Window.
• Preset: Specific values of Window and level. Auto Level [Image] is the default value when changing a LUT and provides the best visual appearance of a Volume LUT.
• LUT Shape: The mapping (transfer function) between the input values and the display values can be linear, sigmoid and logarithmic. Default value is linear.
• LUT (Volume LUT): A Volume Lookup Table (LUT) is a 3D LUT used to map the grayscale values of a volume dataset to color, opacity and lighting values for visualization. Choosing a LUT from the toolbar or the contextual menu is easier because the LUTs are displayed in an order according to the modality and with a preview.
• allows you to invert the LUT.

Volume Rendering C

This panel contains options for the rendering type and its quality, transparency, lighting, and shading settings.

• Type: Composite is the classic type of volume rendering. The Maximum Intensity Projection (MIP) is the highest intensity voxels (3D pixels) along a ray path are projected onto a 2D plane. Iso surface is a technique to create a 3D representation on a specific intensity threshold.
• Z-axis sampling: The sampling should be large enough to accurately capture the details of the volume data, but small enough to avoid excessive computation time. The default value is calculated according to the size of the volume.
• Opacity: The opacity factor of the voxels. Can be set to more than 100% to modify initial values (lower than 100%) transmitted by the Volume LUTs.
• Shading: Allows to activate the shading. Default value is defined in LUT. The additional options allow you to override the default lighting settings (comes from Volume LUT).

Transform D

Allows you to zoom and rotate along a specific axis

Preferences

From the menu “File > Preferences > Viewer > 3D Viewer”:

OpenGL Support

Information about the graphics card and OpenGL capabilities, see Requirements.

3D Viewer

• Default layout: The preferred layout used when opening the 3D viewer
• Max 3D texture size: The maximum size of the volume according to X/Y (width and height of images) and according to Z (number of images in the stack composing the volume)

Volume Rendering

• Dynamic quality: Allows you to make the render more fluid by reducing its quality (according to the z-axis) when it is rotating or being modified. When the slider is at maximum then there is no more quality reduction.
• Default orientation: The preferred orientation used when opening a volume rendering view. Default is Anterior position by turning 15 degrees to the right and 15 degrees downwards.
• Background color: Defines the background color of the rendering
• Light color: Defines the color of the light during the illumination of the rendering

Video tutorials

• Display an MR scan with an angiography-specific protocol by creating a volume rendering. Then either use the MIP type or choose a 3D LUT and adjust the win/level values.

DICOM ECG Viewer

Displaying electrocardiography data

The ECG viewer is used to display and analyze electrocardiogram (ECG) data in DICOM format obtained from different modalities, such as resting ECGs, ambulatory ECGs, and stress tests.

The viewer can also provide tools for measuring ECG intervals and amplitudes in various formats, such as 12-lead ECGs, 3-lead ECGs, and rhythm strips.

Toolbar A

Actions in the toolbar are:

• Allows you to print the ECG as it is displayed with some basic information (patient/study)
• Show the DICOM metadata of the ECG
• Delete all the measurements (yellow areas in the image above), see Markers

Zoom and Display Format B

The zoom is on several graphic components. The first combo box represents the time, the second represents the voltage, and the slider allows you to zoom in both directions while preserving the aspect ratio.

• Time (X-axis): The number of millimeters per second (by default is “auto mm/s”)
• Voltage (Y-axis): The number of millimeters per milli-volt (by default is “auto mm/mV”)

The Display Format allows you to show the leads in different layouts.

Lead and Cursor information C

Moving the cursor over the ECG displays the following information:

• Lead label: show the minimum and maximum voltage values of a lead
• Cursor: show the current time and voltage values under the cursor

Markers D

The markers are the result of the measurements made on the ECG (yellow areas in the image above). A measurement is done by defining a starting and ending point:

• Start Time: The time in seconds according to the position of the first point
• Start Value: The voltage in milli-volt according to the position of the first point
• Stop Time: The time in seconds according to the position of the second point
• Stop Value: The voltage in milli-volt according to the position of the second point
• Duration: The time elapsed between the 2 points
• Difference: The difference in milli-volt between the start value and the end value
• Amplitude: The maximum variation in milli-volts from the start value to the end value

The actions for making measurements are:

• Action to add a starting point: click
• Action to add an ending point: ctrl+click or right-click

Deleting the measurement in a lead can be done by a middle-click or shift+click. Deleting all bars can be done with the button in the toolbar.

Annotations E

The annotations come from 2 groups of DICOM metadata:

• Acquisition context and Annotations: Attributes which describes the conditions present during data acquisition.
• Annotations: may represent a measurement or categorization based on the waveform data, identification of regions of interest or particular features of the waveform, or events during the data collection that may affect diagnostic interpretation (e.g., the time at which the subject coughed).

DICOM SR Viewer

Displaying DICOM Structured Report

The DICOM Structured Report (SR) viewer is used to display and analyze DICOM SR data. The SR object is a structured collection of content items that represent a report of a diagnostic or therapeutic procedure. The content items are organized in a tree structure, and each item has a relationship with other items.

The viewer displays the content of the SR object in a structured way, allowing the user to navigate through the tree and visualize the content of each item.

Try to open sample SR files Launch

Toolbar A

Actions in the toolbar are:

• Allows you to print the rendering of the SR
• Show the DICOM metadata of the SR

Display SR Header B

The header of the SR object is displayed in a table format with 3 columns containing information about the patient, the study, and the report status.

DICOM SR Tree C

The content of the SR object is displayed in a tree structure. Each node in the tree represents a content item with hierarchical numbering, and the tree structure reflects the relationships between the items.

Some items can have a link to other content items, and the viewer provides a way to navigate through the tree by clicking on the links.

This link can also open a related image which can contain measurements defined in the SR object (e.g. in the image above, clicking on POLYLINE will open the image and display the polyline).

DICOM Audio Player

Playing DICOM AU data

This player is used to play audio data defined by the DICOM AU standard.

Try to open DICOM AU Launch

Toolbar A

Actions in the toolbar are:

• Show the DICOM metadata of the DICOM AU

Play B

The Play button allows you to play and pause. The slicer allows you to navigate through the audio file and display the position in seconds.

Volume C

This slider allows you to adjust the volume of the audio file.

Export Audio File D

The Export Audio File button allows you to save the audio file in the format AU or WAVE.

Draw & Measure

How to draw and measure on images

This panel allows you to draw and measure on DICOM and standard images. The results can be exported:

• For DICOM, in a DICOM Presentation State object.
• For standard images, in an XML File in the same directory of the image (when exporting the images in non dicom file format). The XML file is automatically loaded when the image is displayed in the standard 2D Viewer.

Draw & Measure Panel

When clicking on of the vertical button , the panel is displayed on the right side of the viewer. This panel is divided into 4 parts.

Measurement tools A

Select a measurement tool by clicking on one of the buttons and then draw on the image. Note that the previous action will select automatically the drawing action in the mouse left button.

The first button is the selection tool that allows you to select, resize and move the graphic objects.

By selecting one or several graphic objects, you can change properties (e.g. color, line width) or copy/paste with the contextual menu. You can also delete the selection with the delete key or . See other shortcuts for graphics.

Drawings B

The drawing buttons allow you to add text and graphic as annotations. These graphics objects do not display measurement values and do not appear in Selected Measurement D.

Graphic Options C

• Line color: The default line color when drawing new graphic object. The default value is yellow. The opacity can be changed from the transparency or alpha slider of the different color models in the color picker.
• Line width: The default line width.
• Draw only once: After drawing a graphic object, the tool is automatically set to the selection mode. If unchecked, the tool remains active for drawing a new graphic.
• Pixel statistics: Show statistics of the pixel values within the shape. Only for graphic objects with a closed shape (e.g. rectangle, ellipse, polygon).
• Unit: The unit of the image spatial calibration. If no calibration is defined, the unit is pixel. See also How to change the spatial calibration.
• More options: The preferences to change more display options (see preferences).

Selected Measurement D

The selected graphic E created with a measurement tool is displayed in the table. The table shows the shape properties according to the measurement type (and its units in square brackets if exists).

When Pixel statistics is checked, some statistics are displayed in the table only for graphics with a closed shape (e.g. rectangle, ellipse, polygon). The statistics are calculated from the pixels inside the graphic shape:

• Pixels: The number of pixels inside the graphic shape
• Min: The minimum modality value
• Max: The maximum modality value
• Median: The median modality value
• Mean: The mean modality value
• StDev: The standard deviation is a measure of the dispersion of the values
• Skewness: The skewness is a measure of the asymmetry of value distribution
• Kurtosis: The kurtosis is a measure of the “tailedness” of value distribution

Preferences

From the menu “File > Preferences > Draw & Measure”:

Drawings

It lets you change the graphic properties when drawing new graphics, since Version4.3.0.

• Line color: The default line color. The default value is yellow. The opacity can be changed from the transparency or alpha slider of the different color models in the color picker.
• Line width: The default line width.
• Fill shape: When checked, the shape is filled with the line color.
• Fill opacity: The opacity of the interior of the shape, relative to the opacity of the line color. The default value is 100%. For example, if the line color has an opacity of 80% and the fill opacity is 20%, then the perceived opacity will be 16% (0.8 * 0.2).

Labels on image

It lets you change the display options for labels attached to measurement graphics.

• Font type: The default font size of the labels on the image. The default value is Small semibold. Note that the font size is not absolute and is automatically adjusted according to the scale factor.
• Geometric measurement: the measurement types displayed on the image according the graphic type.
• Pixel statistics: the statistics types displayed on the image for graphic objects with a closed shape (e.g. rectangle, ellipse, polygon).

DICOM RT Tools

Displaying radiotherapy information

The RT Tool appears on the right panel when a CT exam (when linked with DICOM STRUCT, PLAN and DOSE) is displayed. Since Version4.1.0 a specific configuration in config.properties is no longer required.

How to display structure and iso-dose

In order to display the structures in overlay on the image, apply the following points (see in the image below):

1. InfoOptional When selected, it allows you to force the DVH calculations. Otherwise, it is calculated only if some information is not available in the DICOM files.
2. Click on “Load RT” button to load DICOM STRUCT, PLAN and DOSE associated the CT images. Once loaded, the button becomes inactive.
3. InfoOptional Select a structure if there is more than one.
4. InfoOptional Select a plan if there is more than one.

For displaying the iso-doses, apply the following points (see in the image below):

1. Select the Isodoses tab
2. Check the Isodoses root node which is not activated by default
3. InfoOptional Adjust the graphic opacity

How to display DVH

• Select one or several structures. Note: the Structures root node must be selected.
• Click on the button “Display DVH chart”
• Right-click on the chart to print or save as a PNG image or vector files such as SVG or EPS.

DICOM Attributes

How to display DICOM attributes

The DICOM attributes can be displayed either by:

• selecting the “Dicom Information” layout from the layout dropdown button A
• clicking on the “Dicom Information” button in the toolbar to open a detached window B

When Weasis opens particular DICOM files (e.g. PDF and video) with an external viewer, the DICOM attributes can be viewed from the thumbnail context menu (see image below).

How to find a specific DICOM attribute or value

The Dicom Information window contains two tabs:

• Limited DICOM attributes: List of the main attributes assembled in several groups.
• All DICOM attributes: List of all the attributes where each data element is displayed within four columns (Tag ID, VR, Tag Name and Value)

In the image above, we are looking for the word “date”. Here are the steps:

1. Select All DICOM attributes tab for having all the attributes.
2. Enter the word you are looking for.
3. Use the arrows to navigate into the highlighted results. The button on the far right allows you to limit the results to positive ones.
4. The navigation shows the current result in highlight mode.

Using in the toolbar allows you to filter the results. This can be useful to keep the focus on certain elements when scrolling through a stack of images (only possible with layout A).

Lookup Tables (LUT)

How to handle Color and DICOM LUTs

A DICOM file can contain one or more LUTs. The DICOM pipeline for rendering images contains a number of stages where the LUTs are applied. There are 4 types of Lookup Tables (LUTs) in DICOM:

1. The Modality LUT is used to transform the pixel values into the values of the modality (e.g. Hounsfield for CT).
2. The Values of Interest (VOI) LUT is used to transform the modality values into a visible range that enhances specific anatomical structures or pathological conditions.
3. The Presentation LUT is used to transform the intensity values into P-Values (presentation values are device-independent values related to human perception).
4. The Palette Color LUT is used to transform the intensity gray values into color values with a pseudo color LUT.

Windowing and Rendering

The Windowing and Rendering is a panel in the Image Tools of the DICOM 2D viewer. Some of the options described below are also available in the Lookup Table toolbar, in the main menu and in contextual menus.

• Window: The range of pixel intensity values. The value can be changed when Window/Level is selected in mouse actions or by using the slider.
• Level: The center of the range defined by Window. The value can be changed when Window/Level is selected in mouse actions or by using the slider.
• Preset: The possible items ordered according to the following list:
  • Empty item when the Window and level values are changed manually from slider or mouse actions.
  • Window and level values or VOI LUT data from the DICOM file (ending with [DICOM]). The default value is the first [DICOM] item if exists, otherwise Auto Level [Image].
  • Auto Level [Image] (always visible) which is the Window and level related to the full range of the pixel values
  • Specific values of Window and level for a modality type (e.g. Lung for CT)
• LUT Shape: The mapping (transfer function) between the input values and the display values can be linear, sigmoid and logarithmic. Default value is linear.
• LUT: A pseudo color LUT used to map the grayscale values to color. Default (image) is the original image color model. Choosing a LUT from the toolbar or the menus is easier because the LUTs are displayed with a preview.
• allows you to invert the LUT.
• Filter: The 2D filter is applied to the image before the LUT. The filter can be used to enhance the image quality or to highlight specific structures. The default value is None.

Build DICOM KO and PR

How to build and export DICOM KO and PR

Key Object Selection (KO)

• In order to display KO Toolbar, select in the main menu: View > Toolbars > Key Object Selection Toolbar

• When a DICOM KO is loaded then it appears in the explorer menu (1) or it can be selected from the icon on the right of the view (6).

• Click on the star icon (3) to add the key image or press ‘k’ to create in a new KO.

• Other actions:

  • Apply a KO (2)
  • Filter to obtain only the key images defined in the selected KO (4). This means only key images will be visible when scrolling into a series.
  • Create a new KO (or based on another one) or delete KO (only the ones created by Weasis) (5)

Presentation State (PR or GSPS)

• Apply PR loaded from a DICOM file (1) : Since Version2.6.0 PRs are not applied to the image by default (requires to select the right icon (2) over the image). In order to apply the most recent PR by default, change it from the main menu File > Preferences (Alt + P) and check “Apply by default the most recent Presentation State”, or in the default preferences.
• Create a new PR: Any type of annotations (Drawings and Measurements) can be exported in a DICOM Presentation State. Image presentation actions (zoom, calibration, W/L, LUT…) are not yet possible to export into PR.
  

Exporting Key Object Selection or Presentation State

• In order to export KO or PR, select the DICOM Export icon or from the main menu File > Export > DICOM
  

1. Select the export type (locally or remotely)
2. Choose the exporting options (series created by Weasis have the flag “NEW”)
3. Select the patient/study/series/instance to export
4. Export the selection and close the Window

DICOM SEG

Displaying DICOM Segmentation

Since Weasis Version4.3.0, this panel lets you display the contents of a DICOM SEG file superimposed on the image. It also lets you modify the transparency of specific regions (label defined by a color).

DICOM SEG can be generated by AI frameworks to represent the results of segmentation algorithms applied to medical images.

How to display DICOM SEG

In order to display the DICOM SEG regions in overlay on the image, follow these steps (see in the image below):

1. Open the DICOM series with a link to a DICOM SEG object. This link is visible by the segmentation icon in the lower right-hand corner of the thumbnail.
2. Once the image is displayed, you can click on of the vertical button to show the Segmentation panel on the right side of the viewer.
3. A DICOM SEG file is represented by a selected item in the combo box and its list of regions below. By default, all DICOM SEG files linked to an image are displayed.
4. Select one or several regions to display for the selected DICOM SEG (3). Several regions are grouped together when they share the same first name. Note: the parent node must be selected to display the child regions.
5. Adjust global graphic opacity (border and interior)

AI DICOM Objects

DICOM objects generated by artificial intelligence

Artificial intelligence (AI) frameworks can produce various DICOM objects for different purposes. Here are some common DICOM object types produced by AI frameworks and how they are handled in Weasis (see Info window).

DICOM Secondary Capture (SC)

This type of object represents secondary images where the AI has embedded information in the image pixels. These images may include annotations, measurements, or other enhancements to the original image data.

DICOM Segmentation (SEG)

These objects represent the results of segmentation algorithms applied to medical images. Segmentation involves partitioning an image into multiple segments to simplify its representation for analysis or display. AI frameworks can produce SEG objects containing segmentations of anatomical structures, lesions, or other regions of interest.

DICOM RTSTRUCT

This type of DICOM object is originally used to represent structures delineated on CT images for radiotherapy treatment planning. Some AI frameworks may produce DICOM RTSTRUCT objects (geometric shapes) instead of DICOM Segmentation (pixel-based).

TotalSegmentator automatically segments over a hundred anatomical zones on CT images. When the result is saved in DICOM RTSTRUCT (since version 2), the segmentation result can be displayed directly in Weasis:

DICOM Structured Report (SR)

AI frameworks can generate structured report containing the results of their analysis. These reports typically include structured information about findings, measurements, observations, and interpretations derived from medical images or other data.

DICOM Encapsulated Documents

AI frameworks may produce DICOM objects containing encapsulated documents such as PDF reports, text documents, or other non-image data related to medical imaging studies.

DICOM Presentation States

Presentation states define how images should be displayed, including display parameters such as window width, window center, and image orientation. A Grayscale Softcopy Presentation State (GSPS) object is used to display annotations and graphics that overlay on a displayed image. AI frameworks might generate presentation states to specify how images should be displayed based on their analysis results or to display graphics overlays on images.

DICOM Enhanced Objects

Enhanced DICOM objects contain additional information. AI frameworks might produce enhanced DICOM objects to include additional annotations or other enhancements to the image data.

Zoom

Zoom tool

The zoom tool can be associated with one of three mouse actions . In the image below the zoom tool is associated with the middle mouse button. See also zoom preferences.

The zoom factor can be modified from different locations:

• By dragging the cursor over the image with the configured mouse button
• By scrolling the mouse wheel when configured
• By selecting an item in the zoom dropdown button in the toolbar
• From the context menu: right-click on the image > Zoom
• Form the slider in the image tool panel
• Using Keyboard Shortcuts (Ctrl + Plus (+), Ctrl + Minus (-) and Ctrl + Enter) on the selected view

The context menu and the toolbar button allows you to select different zoom factor:

• Actual pixel size : display the image at a 1:1 ratio, where each pixel in the image corresponds to one pixel on the screen
• Real world (see below)
• Resize to best fit : scaling the image to make it fit the view area as closely as possible

Real-world zoom

The real-world zoom allows displaying the content of the image at the same size of the real objects.

The feature requires calibrating the screen where the image is displayed. From the main menu, open File > Preferences (Alt + P) > Monitors and click on Spatial calibration. Then enter a value that matches to the line length or the diagonal length of the screen.

Magnifying lens

The magnifying lens can be activated from the toggle button of the zoom toolbar (see the image below). It has several parameters accessible from the context menu.

This lens can be used in many situations, for instance:

• to magnify a specific area
• to compare two images from the same series (select Freeze image)
• to display a specific area without the drawings (Unselect Show Drawings)
• to compare different values of Window/Level (select Freeze parameters - see image below)

Parameters of the context menu:

• Synchronize to parent zoom: When this option is activated, the zoom factor of the lens is permanently adjusted to the zoom factor of the main image (meaningful when using freeze parameters).
• Show Drawings: Displays in the lens the visible drawings.
• Magnify: Allows to select a zoom magnitude.
• Image: Freeze parameters allows you to keep the current image processing (c.f. Window/level, LUT or filter) and Freeze image allows you to keep the current image and its parameters.

Histogram

Displaying Histogram

Displaying the histogram allows you to view the distribution of the modality values.

To open the histogram, select the “Histogram” layout from the Layouts dropdown button (see the image below).

General histogram parameters:

• Channel: With gray images only the Luminance channel is available. With color images, you can choose one of the following color models: RGB, HSV and HLS.
• Bins: The bins are the intervals values of pixels. By default, this number is calculated by the max value minus the min value and cannot exceed 512. The value entered must be between 64 and 4096.
• Statistics: Show the statistics of the histogram which allow you to analyze and to compare images or image regions in a quantitative way. For the definition of the statistics parameters, see graphic Pixel Statistics.

Display histogram parameters:

• -/+: shrink/strech the y-axis scale (the number of occurrences)
• Accumulate: Display a cumulative histogram
• Logarithmic: Show the number of occurrences in a logarithmic scale (y-axis).
• Show intensity color: Show the bin with the LUT colors, otherwise in black.
• Reset: Set the default parameters

Image orientation

Interpretation of the orientation

The orientation of the DICOM images is displayed by one or more uppercase letters in the middle on the top and left of the view.

If Anatomical Orientation Type (0010,2210) attribute is absent or has a value of BIPED, anatomical direction is:

• A: anterior
• P: posterior
• R: right
• L: left
• H: head
• F: foot

If Anatomical Orientation Type (0010,2210) attribute has a value of QUADRUPED (since Version4.1.0), anatomical direction is designated by:

• LE: Left
• RT: Right
• D: Dorsal
• V: Ventral
• CR: Cranial
• CD: Caudal
• R: Rostral
• M: Medial
• L: Lateral
• PR: Proximal
• DI: Distal
• PA: Palmar
• PL: Plantar
  

Orientation in 2D multiplanar reconstruction (MPR)

The image below shows the 3 views of the orthogonal MPR. The uppercase letter at the left or at the top designates the orientation of each multiplanar view whose type (axial, coronal, sagittal) is defined at the bottom.

Print

Build the image selection to print

The image selection to print must be prepared before calling the print function. If you need to print more than one image per page, choose a layout from the dropdown button in the toolbar (1).

To fill the layout with images you can change the synchronized mode of series (2):

• with Default Tile selected, all the views will be filled with the same series. Each view has a new image of the series stack (n + 1).
• with Default Stack selected, drag and drop a series into each view and select independently which image you want to display.

Select a print mode

Standard Printer

From the main menu, open File > Print > Print 2D viewer layout (P).

The meaning of the standard print parameters:

• Image position: the position of the image in the print area.
• Image DPI: the print resolution in dot per inch (Default value is 150). Higher DPI means higher resolution.
• Print image with annotations: Allows to print the annotations defined in the Display panel.
• Print only the selected view: When this option is checked, only the selected view is printed (view with an orange border). Otherwise, all the views of the layout are printed.

DICOM Print

From the main menu, open File > Print > DICOM Print.

In the DICOM Print dialog, you can manage several configurations. For the options meaning, you can refer to the above parameters and the DICOM print pages.

Spatial Calibration

How to change the spatial calibration

When the image does not contain a default spatial calibration and it contains a ruler (or other element allowing to determine a known distance) then you can apply a calibration manually:

1. Select a line in the Measurement Tool
2. Draw a line on an object with a known distance
3. Right-click on the selected line and enter the distance on the Manual Calibration window

Changing spacial calibration with Weasis 1.1.3

Styles and themes

Change the appearance of the user interface

How to apply another theme

From the main menu, open File > Preferences (Alt + P) and select the desired theme and click on “show” to see a partial preview (1).

How to scale the user interface

It is recommended to adapt the scale factor to the one of the system (2). In this way, Weasis will scale on HiDPI displays as the operating system. On Windows it is the Display Scaling preference and on Linux it is either the display scaling factor or the text scaling factor.

However, the scaling factor can be increased (or even decreased) independently of the system. That means all the elements of the graphical interface will be adapted (fonts, icons, graphic components…).

Changing the default theme or scale factor

See preferences

Translation

How to change the language and regional settings

Switching from the user interface

From the main menu, open File > Preferences (Alt + P) and select the desired language and the regional format. The languages available in the list can be partially translated. In this case you can participate in the translation directly from a web portal.

Changing the default locale settings

If you need to change the default settings, please see the preferences.

Logging

Configure and view log files

The log folder that can be opened from the menu “Help > Open the logging folder” (since Version4.1.0) contains two types of log:

1. A boot log file (boot.log) is always written since Version3.5.0
2. Rolling log files (default.log) that need to be activated in the preferences dialog (see below How to configure the rolling log files)

Boot log files

The boot log file is used to trace the startup configuration to ensure that the application starts with the correct input parameters and configuration. This type of logs is interesting if the application doesn’t start, crash at startup, or if there is a problem with the startup preferences.

How to configure the rolling log files

• From the main menu “File > Preferences > General” enable “Rolling log” to activate writing to files
• Enter the maximum of File numbers for rolling log (by default 5)
• Enter the maximum size of each rolling file (by default 10 MB)
• Select a log level which defines the verbosity of the traces (by default DEBUG)
• Select a stacktrace limit which represents the number of lines (by default no value). No value is recommended for investigating problems (it means unlimited stacktrace lines)

Proxy server

How to configure a proxy server

Manual configuration from the user interface

From the main menu, open File > Preferences (Alt + P) and select Proxy Server.

The default configuration is Direct connection (no proxy) and by clicking on Manual proxy configuration you can define a custom proxy server (in the image below, a local proxy like Squid).

In order to fill in the fields, you must refer to the Java documentation.

Configuration at launch

For setting JVM properties at launch, the selection in user interface must be Direct connection (no proxy) or configuration at launch.

Examples of configuration:

• Set the default system proxy

  -Djava.net.useSystemProxies=true

• Set a local proxy like Squid

  -Dhttps.proxyHost=127.0.0.1 -Dhttps.proxyPort=3128

• Set a proxy in specific domain

  -Dhttps.proxyHost="proxy.mydomain.com" -Dhttps.proxyPort="8080" -Dhttp.proxyHost="proxy.mydomain.com" -Dhttp.proxyPort="8080" -Dhttp.nonProxyHosts="\*.mydomain.com|localhost" -Dhttp.proxyUser="user" -Dhttp.proxyPassword="password"

Dicomizer

How to convert images into DICOM files