This guide explains how to use the caBIG® Annotation and Image Markup (AIM) Template Manager for AIM Information Model Version 3.0. The intended audience for this guide is a biomedical researcher familiar with the AIM information model.
Topics in this guide include: |
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The AIM Template Manager allows you to generate a set of well-defined questions and answer choices to facilitate collecting information for a particular purpose, such as a The Cancer Genome Atlas Glioblastoma (TCGA GBM) study. These questions and answers are contained in an AIM XML template file that you can import into an AIM-enabled application. Aided by the information in the XML file, users of the AIM-enabled application can then annotate medical images using a controlled vocabulary and standard template. This results in simple and constrained annotations that are reproducible and consistent. Finally, the AIM-enabled application captures answers and then exports them as an AIM XML document or AIM Digital Imaging and Communications in Medicine (DICOM) Structured Reporting (SR), which can be sent to the AIM Data Service or DICOM storage Service Class Provider (SCP), respectively.
You use the AIM Template Manager to design templates based on a lexicon of standard and user-definable terms. You can then collect multiple templates into template groups. You complete the process by downloading a template group as an XML file to your local computer.
AIM templates are based on the AIM template XML schema, which in turn is based on the AIM 3.0 model (current release).
Imaging reports contain both graphical drawings and medical knowledge in the form of annotations. These annotations are stored as unstructured text and separated from graphical drawings, which are typically in a proprietary format on an imaging system. Extracting this valuable medical information and combining them with drawings on another system is time-consuming and cumbersome to filter and search.
The AIM model begins to solve this problem by capturing the descriptive information of an image with user-generated graphical symbols placed on the image into a single common information source. AIM captures medical findings using standard vocabularies such as RadLex, SNOMED CT, DICOM, and user-defined terminology. Image information captured in the AIM model includes the anatomic entity and its characteristics, imaging observation and its characteristics, and inference. However, existing vocabularies used to describe medical images contain thousands of terms that make it difficult for users to find and then include them in their AIM annotations.
An AIM template consists of a set of related questions for a study. It captures the name, version, description, UID, controlled term applied to the template, authors, and creation date of a template. It also has one or more components. Each component represents a study question that may have one or more answers. Components can be any of the following: anatomic entity, imaging observation, inference, and calculation.
Both anatomic entities and imaging observations are also described by their associated characteristics. Anatomic entity and imaging observation characteristics inherit the attributes of their respective component. Characteristics have annotator confidence that allows a user to enter a level of user’s confidence answering the question in terms of a percentage. A characteristic may also have a quantification value.
The AIM Template Manager automatically saves your work after each selection you make. An animated image appears to indicate when a save is occurring. |
A template group is a container that holds individual templates.
To add a template group
Deleting a template group does not delete the templates within it.
To delete a template group
You can edit the name, version, description, and author of a template group.
To edit a template group
You can create a copy of a template group to make it easier for you to customize it.
To copy a template group
You can upload a template group you downloaded in the past or received from someone else.
To upload a template group
You can download a template group you create in the AIM Template Manager and then share it with others or save it for future use.
To download a template group
When you design a template, it is helpful to keep the purpose in mind. A template structures how users will enter information into an imaging application. The following table may help make the connection between the AIM Template Manager and information entered into an imaging application.
AIM Template Manager Concept |
Annotation Concept |
---|---|
Component |
Item being annotated; for example, Tumor Location |
Characteristic |
Descriptive element of that item; for example, Site of Tumor Center |
Allowed Term |
Word that may be used to describe the descriptive element; for example, Frontal lobe |
The AIM Template Manager automatically saves your work after each selection you make. An animated image appears to indicate when a save is occurring. |
To create a template
Below the Template Components panel, click to expand all of the template components to see their characteristics or click to collapse the characteristics and just see a list of components. Within the template component row, click the same buttons to expand or collapse individual elements of the component. |
To add a component to a template
Field |
Description |
---|---|
Label |
Double-click this field to add a label. A label becomes a heading in the image annotation form that users complete once the template is imported into an imaging application. For example, "Lesion". |
Description |
Explanatory text about the component; for example, "Select the type of lesion". |
AIM Class |
Select an AIM class from the list. As the image below of the expanded list shows, AIM class options are Anatomic Entity, Imaging Observation, Inference, and Calculation. |
Min |
The minimum number of times the template will allow users this select this term when they annotate an image. |
Max |
The maximum number of times the template will allow users to select this term when they annotate an image. |
Display |
Select this box to display this component in the template. |
Confidence |
Specify the confidence interval for the value users will enter for this component. Expected values are 0 through 100. |
Authors |
The AIM Template Manager user who created this component. |
Calculation components require that you add not only the basic information about the component but also additional information about the calculation.
To add a Calculation component to a template
The AIM template requests the following information about a Calculation component.
Field |
Description |
---|---|
Description |
Explanatory text about the component |
MathML |
An optional mathML representaion of the calculation. |
Algorithm Name |
A name of the algorithm used. |
Algorithm Version |
Information describing a version of algorithm. |
When you add an Anatomic Entity or Imaging Observation component to your template, you may add one or more characteristics to it. While the component entry itself results in a heading once you import the template into an imaging application, the characteristics serve to describe the component. For example, the component might be "Lesion" while some of its characteristics might be "Enhancement Quality", "Proportion Enhancing", "Proportion nCET", and "Proportion Necrosis".
Calculation components also require additional information but it is associated with the component itself and not a separate characteristic. Inference components do not have associated characteristics.
To add a characteristic to a component
Field |
Description |
---|---|
Label |
Double-click this field to add a label. A label becomes a heading in the image annotation form that users complete once the template is imported into an imaging application. |
Description |
An optional description of the characteristic. |
Min |
The minimum number of times the template will allow users this select this term when they annotate an image. |
Max |
The maximum number of times the template will allow users to select this term when they annotate an image. |
Display |
Select this box to display this component in the template. |
Confidence |
Specify the confidence interval for the value users will enter for this characteristic. Expected values are 0 through 100. |
Authors |
The AIM Template Manager user who created this characteristic. |
When users of your AIM template answer template questions, you can offer a list of standardized terms for their answers. You can either manually add an allowed term or use one you have Imaging:added to a lexicon in the AIM Template Manager.
To specify a characteristic's allowed terms
To add additional allowed terms, click to add another row. Similarly, to delete an allowed term associated with a characteristic, select it and then click |
If you cannot scroll any further to the right to see all of the fields of an allowed term, you can hide the Search Lexicon Terms panel. Likewise, you can show a hidden panel. Each panel in the AIM Template Manager has a small arrow in the middle of it, shown below, that you can click to show or hide it. |
Field |
Description |
---|---|
Term |
The allowed term's name. |
Code |
Unique code that identifies the term. |
Source |
Where the term originated. |
Ask if Present |
If you select this box, the template will instruct the imaging application to ask for this information if the characteristic is present. This box is not available for the Inference and Calculation AIM classes. |
To edit a template
To delete a template
You can combing any number of templates in a template group. You may want to do this, for example, to make it easier for you to reference your data during a certain time in a longitudinal study.
This procedure assumes that you have already created both template groups and templates.
To add a template to a template group
To remove a template from a template group
A lexicon organizes the vocabulary that may appear in an AIM template. When you build a template, you can select terms from a lexicon that users of the template will be able to select as answers to template questions. For example, if an AIM template imported into an appropriate application prompted the user to specify the location of a lesion's geographic center, the template could restrict answers to certain allowed terms from the lexicon.
You must first create a lexicon, then add lexicon entries to it. Those lexicon entries become the allowed terms that you add to a template.
The AIM Template Manager automatically saves your work after each selection you make. An animated image appears to indicate when a save is occurring. |
To create a lexicon
To delete a lexicon
To create a lexicon entry
Field |
Description |
---|---|
Code Meaning |
The name of the term you want to use as the lexicon entry. |
Code Value |
The value assigned by the coding scheme designator |
Coding Scheme Designator |
The organization who created this coding scheme. |
Coding Scheme Version |
The version of the coding scheme you are using. |
Description |
A description of the term. |
Lexicon Name |
This field is already populated and is the lexicon you selected before beginning to add an entry. |
To delete a lexicon entry
To copy a lexicon entry
To search for a term