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This guide explains how to use Annotation and Image Markup (AIM) on ClearCanvas Workstation. ClearCanvas

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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.

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  1. Click the Explorer tab.
  2. Click the AIM Data Service 2.0 tab.
    The Explorer tab opened to the AIM Data Service 2.0 subtab
  3. Enter search criteria in the search fields to narrow your search, or leave them blank to retrieve a list of all annotations.
  4. Click Search.
    The Log In dialog box appears.
    AIM Data Service Login dialog box
  5. Enter your user name and password for the AIM Data Service.
  6. Click Log in. The search results appear in the results pane at the bottom of the tab.
  7. Select an annotation from the list of results.
  8. To download and import the annotation into the workstation, do one of the following:
    • Click the Retrieve Selected Annotation button, orRight-click a selected annotation and select Retrieve Selected Annotation from the context menu
    • Right-click a selected annotation and select Retrieve Selected Annotation from the context menu.

Creating DICOM Segmentations (new in 4.5)

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).

  1. Select Tools > Preferences > Segmentation.
    The Segmentation tab appears.
    Segmentation tabImage Added
    The DICOM segmentation tool also appears in the toolbar: DICOM segmentation toolImage Added .
     
     Segmentation toolbar highlighted within AIM on ClearCanvas Workstation 4.54Image Added

  2. Use the freehand tool to manually draw a segmentation object: Freehand toolImage Added.

    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.

    Info

    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.
    Image list with information such as Image 6 Frame 1Image Added

    Context menu showing a Rename commandImage Added

  3. Select values in the Segmentation Properties section.

    Segmentation properties including Selected Category, Type, Modifier, Anatomic Region, and Anatomic Region ModifierImage Added

  4. Click Create Segmentation.

  5. When prompted, confirm that you want to create a DICOM segmentation. Note that once you create a segmentation, you cannot modify or delete it.

    Confirm segmentation creation dialog boxImage Added
    You can, however, adjust the opacity level using the opacity slider bar.
    slider bar that allows you to adjust the opacity levelImage Added

  6. 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.

Downloading Images from XNAT

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  1. In AIM on ClearCanvas Workstation, specify the folder where you want to place images you download.
    1. Select Tools > Preferences > Tools.

    2. Click XNAT.
      The XNAT options appear.
      XNAT options include XNAT URL, Auto Import Download Folder, and the number of seconds to check for downloads

    3. 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 .

    4. Click OK.
  2. In the AIM on ClearCanvas toolbar, click  XNAT button.
      XNAT CENTRAL appears.
    XNAT Central.Image Modified
  3. Register for XNAT Central, if needed, and then log in using your XNAT Central name and password.
  4. Click a project name where the images are that you want to download.
    The study's details and subject summary appears. Since you have logged in, you can see the Actions menu options.
    Details and subject summary for a study.Image Modified
  5. Decide if you want to download a single experiment's images or all of the study's images. Downloading a single experiment's images generally takes less storage space and time than downloading all of a study's images.
  6. Download the images.
    1. To download a single experiment's images, do the following.
      1. Click a subject's link.
        The experiments appear.
        list of a study's experiments
      2. Click an experiment's link.
        The scans appear.
        list of an experiment's scans
      3. Select Download > Download Images.
        a single session's images listed by scan
      4. Select the download file type and which scans you want to download. The more scans you select, the longer the download will take and the more time it will take to download them.
      5. Click Download.
    2. To download all of a study's images, do the following.
      1. Select Actions > Download Images.
        imaging data download dialog box listing all of a study's sessions

      2. Confirm the sessions and image data you want to download, select the download format.

      3. Click Submit.

    3. When your browser prompts you to save the file from XNAT, select Save > Save As to specify the folder where the download should go. Make it the same path as that which you specified in step 1c in AIM on ClearCanvas Workstation.
  7. Check your destination folder for the images you downloaded. The downloaded file will be automatically uncompressed or unzipped and DICOM images in the zip file will be imported. The file will be deleted after importing DICOM files is done. 

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  1. Select Tools > Preferences > AIM.
    The Options dialog box appears.

    AIM options dialog box

  2. Specify any of the following AIM preferences.

    OptionDescription
    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 LocallyIf 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 InformationIf selected, user credentials need to be entered before creating an AIM annotation document.
    Require Graphic Markup in AnnotationIf 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 CalloutsChange the image used when you create text callouts.
    Templates FolderIf entered, the directory will be used to search for AIM template XML documents.

  3. Click Apply.

Specifying Toolbar Preferences

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The following table describes four AIM tools that are available on the AIM on ClearCanvas Workstation.

Tool

Name

Description

AIM Template buttonImage Modified

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 buttonImage Modified

AIM Object Locator

Depicts available AIM objects in the currently displayed study without searching through every image in the study or series.

AIM Details buttonImage Modified

AIM Annotation Details

Provides the ability to view specific areas of a selected graphic markup for an existing annotation.

Closed Polygon Markup buttonImage Modified

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.

AIM Template Tool

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.

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Composite image showing XML folders on a hard drive and AIM Annotation dialog box
Figure 7. Importing an AIM Template

Locating Missing Answer Choices

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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.

Question mark icon next to the Create Annotation button in an imported AIM template

Enforcing Markup Requirements

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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 ConditionVerification Condition
Template has multipoint geometric shapeLine or angular markup has to be drawn on image
Template has polyline geometric shapeRectangular or polygonal markup has to be drawn on image.
Template has circle or ellipse geometric shapeElliptical markup has to be drawn on image.
Template has point geometric shapeCross 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.

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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.

AIM annotations for an imaging studyImage Modified

Using the National Biomedical Imaging Archive (NBIA) Data Service

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Search NBIA dialog box
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.

Results with all available columns selected.Image Modified