This version of the plugin is based on OHIF Viewer 2.0 and uses the React JavaScript library.

This plugin integrates the OHIF viewer into XNAT. Version 3.0 comes with a suite of annotation tools, and allows users to import/export ROI Contours and Segmentations to ROICollection Assessors on XNAT. Up to date viewer bundles are available in the downloads area.

Version 3.0 of this plugin is distributed as a single jar file. If upgrading from v2.1 then both ohif-viewer-2.1.0.jar and xnat-roi-2.2.0.jar need to be removed from the plugins directory of XNAT

Note full patch-by-patch changes are available in the CHANGELOG.

This release is built around the XNAT 1.8 specification and is not compatible with XNAT 1.7.x or any previous version.

A major feature of 3.0 is the inclusion of a set of tools for annotating regions of interest within XNAT and storing these in the XNAT database for use in processing pipelines. Using the ROI Upload Assistant, one may also upload regions of interest stored in DICOM RTSTRUCT, DICOM SEG and AIM 4.0 Image Annotation Collection formats from external sources to XNAT. These will be automatically indexed and importable in the viewer.

If a scan contains segments or ROIContours, appropriate icons will be displayed under the thumbnail in the scan list.

The ROI Contour tools can be used to create and modify contour-based regions of interest. Sets of 2D contours make up named 3D contours which specify a region. One of more 3D contours make up an ROICollection which can be imported/exported from/to XNAT.

• The Draw tool allows the user to draw a 2D contour via two methods:
  • Polygon mode: Clicking on several points with the Draw tool and then clicking back at the origin allows the user to draw an accurate polygon.
  • Freehand mode: Click-dragging with the freehand tool allows a user to draw a freehand contour.
• The Sculpt tool allows users to modify an existing ROI by pushing and pulling it with a disk.
  • Double click near a contour with the sculpt tool to select it for editing.
  • Move the mouse nearer/farther from the region to use a smaller/larger disk size for sculpting.
  • Click and drag to use a the selected size disk to sculpt the contour.

ROI Contours may be managed and imported/exported to XNAT via the Contours sidebar interface. The sidebar also allows you to toggle:

• Interpolation - Whether intermediate contours should be linearly interpolated when drawing, such that you only need to manually delineate every few frames.
• Stats - Whether to display the labels and 2D statistics of each contour on the viewport.

The Segmentation tools may be used to create and modify labelmap-based regions of interest. Collections of voxels marked with a particular label comprise 3D segments which specify a region. One or more segments make up an ROICollection which can be imported/exported from/to XNAT.

• The Manual brush tool allows the user to paint the labelmap using a circular brush.
• The Smart CT brush tool allows you to select a tissue type, or set a custom Hounsfield Unit gate, to quickly segment CT scans by roughly scribbling over a region whilst only painting in the desired tissue.
• The Auto brush tool sets the threshold for the gate of a brush stroke (mouse drag) by the minimum and maximum pixel values present within the brush cursor when the mouse is pressed down.

Segments may be managed and imported/exported to XNAT via the Segments sidebar interface. The sidebar also allows you to set:

• The tissue type (gate) used by the Smart CT brush tool. Or a custom gate.
• The hole-filling and island removal settings for the Smart CT and Auto brush tools.

The plugin adds a new assessor datatype, the ROICollection.

• ROICollections are containers for common contour-based and labelmap-based segmentation formats.

  • Currently supports DICOM RTSTRUCT, DICOM SEG and AIM 4.0 Image Annotation Collection formats.
  • ROI Contour annotations drawn in the viewer may be exported to XNAT, generating an ROICollection containing an AIM representation and an RTSTRUCT representation.
  • Segment annotations drawn in the viewer may be exported to XNAT, generating an ROICollection containing a SEG representation.
  • The ROI Upload Assistant may be used to upload RTSTRUCT, SEG and AIM to XNAT, which can then be viewed/modified in the viewer.

• ROICollections have a custom datatype page, which list the individual regions within the collection.

• Individual regions contained within an ROICollection are stored in Hibernate tables within XNAT, and so are searchable.

• A revamped routing system for mapping XNAT concepts onto OHIF concepts means the viewer no longer needs to sit in an XNAT parent window.
• Left clicking View Session/View Subject will open the viewer in the active window.
• Middle/Right clicking View Session/View Subject will open the viewer in a new tab/window depending on browser configuration.

• Using the sync toggles at the top right of each viewport, one can synchronize scans to scroll together.

  • The 'More/Sync Settings' menu has the option to set all viewports to be synced by default.
  • The 'More/Sync Settings' menu lets the user switch the synchronization strategy to operate via image position or by frame number. Image position is the default.

• The Smooth toggle at the top right of each viewport allows the user to toggle voxel interpolation (previously always on).

  • Turning smoothing off for very low resolution images can sometimes help with labelmap delineation.
  • Smoothing is on by default.

• Clicking View Subject on a Subject page will now open up a subject-wide viewer session.

• In Subject view, the scan list contains a collapsible list of scans for each Session. You can view and annotate scans from multiple sessions simultaneously.

• When you annotate ROIs and export them back to XNAT, they will automatically be stored under the appropriate session.

• If metadata isn't present for all sessions, a dialog will appear telling the user its being generated. Once generated, the user will automatically be redirected to the subject view.

Parent Project - the original source project.

Target Project - the project the session is shared into.

• A session shared into a target project can now viewed by a user who only has access to the target project.
• If multiple sessions belonging to a particular subject are shared into a target project, a user in the target project may open a shared Subject view.
• ROICollections which are shared into the target project are able to be imported into the appropriate shared views.
• If a user in the target project has write access to the parent project, the export button will show in the Contour and Segment interfaces, and will push annotations back to the parent project.

A navigation bar can now be accessed by opening the left-hand XNAT Nav tab in the viewer.

• The navigation bar allows the user to easily switch to a different XNAT project/subject/session, allowing one to segment many scans without leaving the viewer interface.
• Under 'This Project', the active project is displayed, with the active subject/session view highlighted yellow.
• You may navigate to subject/session views of other projects by expanding the project under 'Other Projects'.
• If a subject/session is shared from another project, the projectId of its parent is also displayed.
• If a XNAT Session contains ROICollections, the quantity of ROIContour and Segment collections will be displayed under the session name within the tree view.
• If a user has unsaved annotations, they will get a warning confirmation before being able to navigate to a different view.
• The navigation bar fetches data about Projects/Subjects/Sessions on demand, resulting in a quick and responsive UI, often capable of navigating XNAT much faster than navigating through the standard XNAT interface.

• The /viewer XAPI has these end points:
  • GET /viewer/projects/{projectId}/experiments/{experimentId}/exists - returns 200 if JSON metadata exists for the specified session.
  • GET /viewer/projects/{projectId}/experiments/{experimentId} - Returns cached JSON metadata for the specified session or generates it if it doesn't exist.
  • POST /viewer/generate-all-metadata - Admin only command to rebuild all JSON metadata on the entire XNAT instance. This operation may take a long time if used on an instance with a large number of sessions.
  • POST /viewer/projects/{projectId} - Admin only command to regenerate JSON metadata for all sessions in the specified project.
  • POST /viewer/projects/{projectId}/subjects/{subjectId} - Admin only command to regenerate JSON metadata for all sessions in the specified subject.
  • POST /viewer/projects/{projectId}/experiments/{experimentId} - Admin only command to regenerate JSON metadata for the specified session. A tool used if automation is down for any reason.
• Missing JSON being generated and cached in the GET request means a user with READ only permissions to a session can view a session without the need for admin/owner/member intervention.

• Full multi-frame support for both primary and secondary multi-frame DICOM, and import/export of DICOM RTSTRUCT and DICOM SEG objects.
• Multiframe images now fetch their snapshot from a cached XNAT resource, avoiding timeout issues with large multiframes.

Touch support is available for easy segmentation of ROI Contours with a stylus/Apple pen, also including:

• Two finger drag-to-zoom
• Three finger scroll

Since the rest of XNAT currently has poor support for mobile browsers, if delineating ROI Contours on a tablet, its best to be linked straight to the first session to be segmented, the XNAT navigation bar within the viewer can then be used to switch views as needed without the need to use the XNAT interface.

• The viewer has been whitelabelled with the XNAT-OHIF logo and the ICR logo at the top left.
• The viewer displays the plugin version number at the top left.
• The Scans left side bar is now open by default.
• Scrollbars have been added to left and right sidebars for users without a mousewheel.
• The series list now displays full 64 character series descriptions and 10 digit series numbers cleanly, with line wrapping prioritising spaces, and otherwise linebreaking where needs be.
• The 'View Session' button has been changed to 'View Images' as the legacy XImgViewer has been removed.

1. Copy the plugin jar, download here, to the plugins directory of your XNAT installation. The location of the plugins folder varies based on how and where you have installed your XNAT. If using xnat-docker-compose, the plugins folder is located at xnat-data/home/plugins relative to the root directory.

2. Restart your Tomcat server with sudo service tomcat7 restart, or docker-compose restart xnat-web if using xnat-docker-compose.

In the likely event you are installing this plugin on an XNAT with an already populated database, all existing JSON metadata will be invalid due to changes in the metadata required by the viewer since plugin version 2.1. The outdated metadata for a session will be automatically regenerated the first time a user views the session but this will involve a short delay while the metadata is created.

An admin may call one of the REST commands in order to initiate a background regeneration of the required metadata. The REST commands have various levels of granularity ranging from single session through single subject, single project to entire XNAT instance. This allows the admin to prioritise metadata regeneration for their most used data. In the case of large data volumes, the REST command may appear to terminate with a time out e.g. a 504 return value. If this is observed, do not resubmit the command as the original server-side processing will continue and this can be monitored in the plugin's log file ohifviewer.log in XNAT's normal logging directory. We recommend only running one metadata regeneration command at a time to avoid IO contention.

The OHIF Viewer XNAT repository is now used as the ohifviewerxnat submodule of this plugin repository.

Checkout the repository:

$ git clone --recurse-submodules https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin.git

If you have a repository already checked out, update submodules:

$ git submodule update --init --recursive

The ohifviewerxnat submodule requires yarn to build. Assuming you have yarn installed on your machine, initialise it in the submodule. yarn install is invoked from within build_plugin.sh.

Build the plugin in one step:

$ ./build_plugin.sh

The plugin jar will be in build/libs.