This guide explains how to use Annotation and Image Markup (AIM) on ClearCanvas Workstation. ClearCanvas is an open-source imaging platform. This guide explains key procedures for creating and working with AIM annotation objects. The intended audience for this guide is a biomedical researcher familiar with the AIM information model.
AIM on ClearCanvas Workstation allows you to work with AIM templates that you created in AIM Template Builder. A typical workflow from template design to application use follows.
You can configure AIM on ClearCanvas Workstation to connect to the AIM Data Service. The AIM Data Service is any set of data services that can accommodate the AIM data model. There is no public AIM Data Service but you can download it from http://imaging.cci.emory.edu/wiki/pages/viewpage.action?pageId=1572968 and then install and maintain it yourself.
Two files, AnatomicRegionAndModifier.xml
and SegmentationCategoryTypeModifier.xml
are used to describe DICOM segmentations that you can create based on the DICOM standard. You may choose to create and import your own descriptions for anatomic regions and segmentation categories. In this case, you must follow XML schemas designed for an anatomic region (https://cbiit-download.nci.nih.gov/aim/releases/Segmentation/AnatomicRegionAndModifier.xsd) and the segmentation category (https://cbiit-download.nci.nih.gov/aim/releases/Segmentation/SegmentationCategoryTypeModifier.xsd).
Use the freehand tool to manually draw a segmentation object: .
When you create a DICOM segmentation object, you draw many drawings on multiple images of the same thing. Assign the same name to each drawing to create a DICOM segmentation volume.
When you create a segmentation on an image, the information about the image and frame number appears in the image list. This information describes a set of images that form a DICOM segmentation volume. |
Select values in the Segmentation Properties section.
Click Create Segmentation.
When prompted, confirm that you want to create a DICOM segmentation. Note that once you create a segmentation, you cannot modify or delete it.
You can, however, adjust the opacity level using the opacity slider bar.
When you create more than one DICOM segmentation, each DICOM segmentation with the same name is grouped together. A name is automatically added to the Name box. You must provide values in the Segmentation Properties section for each DICOM segmentation before you can create a DICOM segmentation.
AIM on ClearCanvas Workstation automatically displays DICOM segmentations on images in studies with DICOM segmentation objects.
You can connect directly to the XNAT database from AIM on ClearCanvas Workstation and find imaging studies to download, then import those studies and work with them.
AIM on ClearCanvas workstation checks for imaging data you have downloaded in XNAT Central at the interval you select in the XNAT options and automatically imports it into the workstation. You can also manually check for downloads by clicking at any time. |
For more information about using XNAT, consult the XNAT technical documentation.
Click XNAT.
The XNAT options appear.
In the Auto Import Download Folder box, enter the path where you want to store downloaded images. Make a note of this folder path for later, when you will specify this same folder path within XNAT .
Confirm the sessions and image data you want to download, select the download format.
Click Submit.
You can specify AIM, Explorer, and Layout preferences. Some common options are described in the following sections.
Specify any of the following AIM preferences.
Option | Description |
---|---|
Send New Annotations to caGrid | If selected, the workstation will send new annotations to the assigned caGrid location. Also see Specifying AIM Data Service Preferences. By default, the Send New Annotations to caGrid option is disabled. You must enable this option in order to have new AIM XML documents sent to the AIM Data Service. If you have neither set the AIM Data Service destination nor enabled the Send New Annotations to caGrid option, you cannot send your existing AIM XML documents to the AIM Data Service. |
Store New Annotations Locally | If selected, the workstation will store a copy of new annotations in the AIM XML format on the local computer. A user can assign where the AIM annotation documents can be stored on the local computer. |
Required User Information | If selected, user credentials need to be entered before creating an AIM annotation document. |
Require Graphic Markup in Annotation | If selected, a user must create at least one graphical drawing on an image before creating an AIM annotation document. |
Reset Template After Annotation Creation | |
Use Crosshairs Instead of Arrows for Text Callouts | Change the image used when you create text callouts. |
Templates Folder | If entered, the directory will be used to search for AIM template XML documents. |
Click Apply.
You can change the size of icons and choose to show all icons on one screen. To do so, select Tools > Preferences > Toolbar. The recommended icon size is medium and it is also recommended that you select the Wrap long toolbars option.
The following table describes four AIM tools that are available on the AIM on ClearCanvas Workstation.
Tool | Name | Description |
---|---|---|
AIM Template | Displays a template based form with a set of questions and choice(s) of answers for each question. A user can import a new AIM template to that location. Create new annotation objects by completely filling out this form and clicking the Create Annotation button. | |
AIM Object Locator | Depicts available AIM objects in the currently displayed study without searching through every image in the study or series. | |
AIM Annotation Details | Provides the ability to view specific areas of a selected graphic markup for an existing annotation. | |
Closed Polygon Markup | Allows creation of a free hand graphical markup. This tool can be used in addition to existing ClearCanvas tools in creating graphical markup. |
To activate the AIM template tool in Figure 1, click the AIM template tool button (#1). If you put the pin down (#2), you can detach the AIM Template tab by putting the mouse pointer at the header (#3) and dragging it out, as illustrated in Figure 2.
Figure 1. Activate AIM Template
Figure 2. Detached AIM Template Tool
When an AIM annotation is created, the following conditions are applied (based on AIM default settings described in Specifying AIM Preferences)
|
The AIM Object Locator tool, depicted in the following image, allows users to see existing AIM instances available in a study. A list of available AIM instances is displayed below the Available AIM Annotations section, which is #2 in the following image. To access this feature and see an AIM annotation, click Show Study, which is #3 in the following image.
The AIM annotation details, as illustrated by the following image, allow a user to examine detailed information captured in an AIM instance. To access this feature, you select an image containing an AIM instance and then click the AIM Details button, as shown in (#1). The AIM Annotation Details panel appears. This panel contains information tabs including Anatomic Entity, Imaging Observation, Calculations, and All Details. The All Details tab (shown in #3) allows a user to see information related to both Anatomic Entity and Imaging Observation and their characteristics.
Import an AIM template XML document by clicking the AIM Template button. Windows Explorer opens the folder you already specified, which is described in Specifying AIM Preferences.
You can import AIM templates that were created using the AIM XML schema version 2 and above into AIM on ClearCanvas Workstation and capture all of the data in the original template. Unlike AIM Template Builder, which updates AIM templates to the current XML schema version, AIM on ClearCanvas Workstation does not convert all of the information in AIM templates created in pre-2.0 XML schema versions. You can open legacy AIM templates in AIM on ClearCanvas Workstation but it is possible that not all of your questions and answer choices will appear. Data is not lost but options controlling the display of questions and answer choices are not automatically converted upon import. You can avoid this problem for legacy AIM templates by first opening the template in AIM Template Builder and reviewing the options set for each question and answer choice. Specifically, do the following
Once you are sure that all of your question and answer choices have the correct options, save and then export your AIM template, then import the template into AIM on ClearCanvas Workstation. |
Figure 7. Importing an AIM Template
You can locate missing answer choices from a question after you import an AIM template. Click on the question mark icon to find out which questions do not have an answer.
Before you can add an annotation to an image, AIM on ClearCanvas Workstation verifies that the annotation you have drawn complies with the rules in the AIM template. AIM on ClearCanvas Workstation verifies new annotations according to the following rules:
Template Condition | Verification Condition |
---|---|
Template has multipoint geometric shape | Line or angular markup has to be drawn on image |
Template has polyline geometric shape | Rectangular or polygonal markup has to be drawn on image. |
Template has circle or ellipse geometric shape | Elliptical markup has to be drawn on image. |
Template has point geometric shape | Cross hair markup has to be drawn on image. |
In addition to verifying specific new annotations, AIM on ClearCanvas Workstation also checks that no additional marks are on the image that the template does not allow.
To begin enforcing markup requirements, do the following:
Author information as depicted in (Figure 8) can be changed. To use this feature, click the User Info button to activate the AIM User Information form. Enter appropriate information and click Save.
The user information will be saved on the workstation for future use. If you are sharing the workstation with another reader, you must change or at least verify that the information in the User Info section reflects your personal credentials. |
The AIM Template Builder is a tool used to create an AIM template XML document.
Figure 8. AIM User Information
A detailed description of a question can be seen by placing the mouse pointer over the first three characters of each feature name, as shown in Figure 9.
Figure 9. Detailed Description of a Question
For a given image in an imaging study that has more than one reader interpreting and creating AIM annotations, the workstation can display every annotation while allowing you to turn off markups from a selected group of readers. Figure 12 depicts an image with three markups from three readers. The markup from reader named qwe-3 was turned off.
A right-mouse click on the image activates a pop-up menu with a Visible AIM Users option to turn readers' markups on or off.
Figure 12. AIM Markup Display
By default, the workstation also displays annotations created by different users in different colors. You can change which colors are used for which user's AIM annotations. To assign a color to a user, go to Tools > Preferences > AIM > Markup.
By default, the Random checkbox (#2) is selected, which assigns a random color to each user's markup drawings. By clearing the Random checkbox, a default color is used instead. Colors may be assigned to a single user's markup drawings by selecting the color next to the user's name in the list.
Click the Add Login button (#3) to add a new user to the list.
Selected users may be removed from the list by clicking the Remove Selected button (#4). Users removed from the list will have their annotations reset to the default color. Select all users in the list by clicking the Select All button (#5). Click the Reset To Default Color button (#6) to reset the color assigned to selected users to the default color.
You can see AIM annotations for an imaging study grouped by image series in the Available AIM Annotations section. The following screen shows two different image series. The first, Axial FSE, includes one AIM instance. The second, Axial T1, includes three AIM instances.
The NBIA Data Service tab, shown below, provides the ability to connect and retrieve studies from NBIA directly within the workstation. Holding the Ctrl key allows you to click and select multiple studies. Right-clicking a search result activates a feature that allows you to retrieve selected studies.
Users can enter search parameters, shown below, based on a single value or multiple values of Patient ID, Patient's Name, Sex, Birth Date, Project name at NCI, Slice Thickness, Study Instance UID, and Modality.
Columns in the NBIA Data Service page can be selected or deselected to display or hide an available result. The following image depicts that all available columns for the service have been selected.