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 DICOM SR, which can be sent to the AIM Data Service or DICOM store 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 model.
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.
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
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. |
Field |
Description |
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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. |
Label |
Double-click this field to add a label. A label becomes a heading in the form users will complete when the template is imported into another application. |
Description |
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AIM Class |
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Min |
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Max |
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Display |
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Confidence |
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Authors |
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