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{:title} {info:title=To Print the Guide}You can send this page to a printer or [export it to PDF or HTML|WikiTrainFAQsTips:Printing and exporting to different formats]. {info} {panel:title=Contents of this Page} {toc:minLevel=2} {panel} {scrollbar:icons=false} |
This
...
guide
...
explains
...
how
...
to
...
use
...
caBIG®
...
Annotation
...
and
...
Image
...
Markup
...
(AIM)
...
on
...
ClearCanvas
...
Workstation.
...
The
...
information
...
presented
...
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.
...
The
...
ClearCanvas
...
workstation
...
also
...
has
...
an
...
extensive
...
user's
...
guide
...
that
...
can
...
be
...
found
...
on
...
the
...
main
...
menu
...
at
...
Help
...
>
...
User's
...
Guide
...
.
...
For
...
more
...
information
...
on
...
AIM
...
and
...
ClearCanvas,
...
go
...
to
...
the
...
following
...
links:
...
...
...
Wiki Markup {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}
...
Setting
...
AIM
...
Data
...
Service
...
Options
...
The
...
purpose
...
of
...
AIM
...
on
...
the
...
ClearCanvas
...
workstation
...
is
...
to
...
connect
...
to
...
multiple
...
AIM
...
Data
...
Services
...
that
...
can
...
accommodate
...
the
...
AIM
...
3.0
...
information
...
model.
...
As
...
a
...
result,
...
these
...
data
...
services
...
are
...
collectively
...
known
...
as
...
the
...
AIM
...
3.0
...
Data
...
Service.
...
While
...
by
...
default
...
the
...
workstation
...
is
...
not
...
configured
...
to
...
connect
...
to
...
any
...
AIM
...
3.0
...
Data
...
Services,
...
it
...
can
...
use
...
the
...
AIM
...
3.0
...
Data
...
Service.
...
An
...
end
...
user
...
can
...
enter
...
any
...
valid
...
URL
...
for
...
the
...
AIM
...
Data
...
Service
...
and
...
click
...
the
...
Save
...
button
...
to
...
have
...
that
...
URL
...
remain
...
on
...
the
...
workstation
...
for
...
future
...
sessions.
Click to configure the AIM Data Service. You can access the data service configuration from the explorer toolbar, shown in Figure 1, or through an opened study's toolbar, shown in Figure 2.
Figure 1. Access AIM Data Service Options from Explorer Toolbar
Figure 2. Access AIM Data Service Options from an Opened Study
Setting AIM Options
To access the AIM settings, on the ClearCanvas menu, select Tools > Options > AIM. When finished, click Apply to commit the changes. This is demonstrated in Figure 3.
Figure 3. AIM Options
Info | ||
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By default, the setting for sending AIM XML documents to the AIM 3.0 Data Service 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, your existing AIM XML documents will not be sent to the AIM 3.0 Data Service. |
A user may change the following AIM options, which are described in Table 1.
Option | Description |
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Send New Annotations to caGrid | If selected, the workstation will send new annotations to the assigned caGrid location. Also see #Setting AIM Data Service Options. |
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. |
Templates Folder | If entered, the directory will be used to search for AIM template XML documents. |
Table 1. AIM Options Setting
Setting Toolbar Options
The ClearCanvas workstation allows a user to change the size of icons and show all icons on one screen. To do so, select Tools > Options > Toolbar. The recommended icon size is medium and you should select the Wrap long toolbars option. See Figure 4.
Figure 4. Setting Toolbar Option
Using AIM Tools
Table 2 describes four AIM tools that are available on the ClearCanvas workstation.
Tool | Description |
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| 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 Details provides the ability to view specific areas of a selected graphic markup for an existing annotation. |
| Closed Polygon Markup tool allows creation of a free hand graphical markup. This tool can be used in addition to existing ClearCanvas tools in creating graphical markup. |
Table 2. Available AIM Tools
AIM Template
To activate the AIM template tool in Figure 5, 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 6.
Figure 5. Activate AIM Template
Figure 6. Detached AIM Template Tool
Info | ||
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When an AIM annotation is created, the following conditions are applied (based on AIM default settings described in #Setting AIM Options)
|
Importing a New AIM Template
Import an AIM template XML document by clicking the AIM Template button, as shown in Figure 7. Windows Explorer opens a predefined folder described in #Setting AIM Options.
Figure 7. Importing an AIM Template
User Information
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.
Info | ||
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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 Manager is a tool used to create an AIM template XML document.
Figure 8. AIM User Information
Detailed Description of a Question
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. Detail Description of a Question
AIM Locator
The AIM locator, depicted in (Figure 10), 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.
Figure 10. AIM Locator
AIM Annotation Details
The AIM annotation details, as illustrated by Figure 11, 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.
Figure 11. AIM Details
AIM Display Markups from Different Users
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 Figure 12. To assign a color to a user, go to Tools > Options > 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.
Figure 13. AIM Markup Display
Viewing AIM Data for Each Image Series
You can see AIM annotations for an imaging study grouped by image series in the Available AIM Annotations section. Figure 14 shows two different image series. The first, Axial FSE, includes one AIM instance. The second, Axial T1, includes three AIM instances.
Figure 14. AIM Data in Each Image Series
Using Data Services
National Biomedical Imaging Archive (NBIA) Data Service
The NBIA Data Service (Figure 15) tab provides the ability to connect and retrieve studies from NBIA directly within the workstation. Holding the Ctrl key allows you to click on and select multiple studies. Right-clicking activates a feature that allows you to retrieve selected studies.
Figure 15. NBIA Data Service
Users can enter search parameters (Figure 16) 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.
Figure 16. Search NBIA Data Service
Columns in the NBIA Data Service page can be selected or deselected to display or hide an available result. Figure 15 depicts that all available columns for the service have been selected.
Figure 17. Select NBIA Data Service Display Columns
AIM Data Service
The AIM Data Service tab (Figure 18) provides the ability to connect and retrieve AIM XML documents from an AIM 3.0 Data Service (see #Setting AIM Data Service Options). It also allows a user to retrieve both AIM documents and studies from NCI's NBIA. Right-clicking activates a feature that allows you to retrieve studies.
Figure 18. AIM Data Service
You can enter search parameters (Figure 19) based on a single value or multiple values of Anatomic Entities, Anatomic Entity Characteristics, the user who created the AIM XML documents, Imaging Observation, Imaging Observation Characteristics, and Study Instance UID.
Info | ||
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A type of AIM XML document, Imaging Annotation, or Annotation Of Annotation, must be selected. The default value is Imaging Annotation.
Figure 19. Search AIM Data Service
Columns in the AIM Data Service page can be selected or deselected to display or hide an available result. Figure 20 depicts that all available columns for the service have been selected.
Figure 20. Select AIM Data Service Display Columns
Additional Information
Follow the links below for more information on how to set up AIM, information on the AIM Template Manager, and AIM Template Manager software.
- AIM Terms and Concepts
- AIM Template Manager User's Guide
- AIM Template Software Setup manual
- AIM Template Creator Software
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Click !worddav57df0c83ca5ade2e7d98688589f03950.png|alt="AIM Data Service button"! to configure the AIM Data Service. You can access the data service configuration from the explorer toolbar, shown in Figure 1, or through an opened study's toolbar, shown in Figure 2.
!worddavfcda97adbd294755d75f9c42f8fdf8cf.png|vspace=4, border=2, alt="Clicking the AIM Data Service button from the explorer toolbar opens the AIM Data Service Options dialog box"!
_Figure 1. Access AIM Data Service Options from Explorer Toolbar_
!worddav64dfe5682737d95dc8419f301dc47efc.png|vspace=4, border=2, alt="Clicking the AIM Data Service button from an opened study opens the AIM Data Service Options dialog box"!
_Figure 2. Access AIM Data Service Options from an Opened Study_
h2. Setting AIM Options
To access the AIM settings, on the ClearCanvas menu, select *Tools* > *Options* > *AIM*. When finished, click *Apply* to commit the changes. This is demonstrated in Figure 3.
!worddav5990348d61f830209d5a4b8a96ef5d2f.png|alt="AIM Options dialog box", vspace=4, border=2!
_Figure 3. AIM Options_
{info:title=Sending AIM XML documents to the AIM 3.0 Data Service}By default, the setting for sending AIM XML documents to the AIM 3.0 Data Service 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, your existing AIM XML documents will not be sent to the AIM 3.0 Data Service.
{info}
A user may change the following AIM options, which are described in Table 1.
||Option||Description||
|Send New Annotations to caGrid |If selected, the workstation will send new annotations to the assigned caGrid location. Also see [#Setting AIM Data Service Options].|
|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.|
|Templates Folder|If entered, the directory will be used to search for AIM template XML documents.|
_Table 1. AIM Options Setting_
h2.Setting Toolbar Options
The ClearCanvas workstation allows a user to change the size of icons and show all icons on one screen. To do so, select *Tools* > *Options* > *Toolbar*. The recommended icon size is medium and you should select the *Wrap long toolbars* option. See Figure 4.
!worddav9fc7a8480ffc46bbe5b7e59dba768737.png|vspace=4, border=2, alt="Toolbar tab of the AIM Options dialog box"!
_Figure 4. Setting Toolbar Option_
h2. Using AIM Tools
Table 2 describes four AIM tools that are available on the ClearCanvas workstation.
||Tool||Description||
|!worddav1a00ecf0b68234ff0474dd9998ae71ee.png|alt="AIM Template button"! |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.|
|!worddav1ff28c9994b0d6f8aabb73039be51b3e.png|alt="AIM Object Locator button"! |AIM Object Locator depicts available AIM objects in the currently displayed study without searching through every image in the study or series.|
|!worddav92230efbdac250e4dc9b8fd919da18f2.png|alt="AIM Details button"! |AIM Details provides the ability to view specific areas of a selected graphic markup for an existing annotation.|
|!worddav48e47f5bbfcf7b4be686d85ef0274981.png|alt="Closed Polygon Markup button"! |Closed Polygon Markup tool allows creation of a free hand graphical markup. This tool can be used in addition to existing ClearCanvas tools in creating graphical markup.|
_Table 2. Available AIM Tools_
h3. AIM Template
To activate the AIM template tool in Figure 5, 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 6.
!worddav751ddf5b92acfef706331113246f9c9e.png|vspace=4, border=2, alt="Explorer window and AIM Template tab"!
_Figure 5. Activate AIM Template_
!worddave15a3e6cc596f65fa53053fb123a15d9.png|vspace=4, border=2, alt="AIM Template tab detached from Explorer window"!
_Figure 6. Detached AIM Template Tool_
{info:title=Important}When an AIM annotation is created, the following conditions are applied (based on AIM default settings described in [#Setting AIM Options])
# A user must answer all questions presented in the AIM Annotation window.
# A graphical markup is required on an image if _Require Graphic Markup in Annotation_ is selected before an AIM annotation can be saved to the AIM Data Service and/or stored locally.
# User information must be entered if _Require User Information_ is selected.
{info}
h3. Importing a New AIM Template
Import an AIM template XML document by clicking the *AIM Template* button, as shown in Figure 7. Windows Explorer opens a predefined folder described in [#Setting AIM Options].
!worddavd03a3a29c9bb39d70b95decf3ca0921b.png|vspace=4, border=2, alt="Composite image showing XML folders on a hard drive and AIM Annotation dialog box"!
_Figure 7. Importing an AIM Template_
h3. User Information
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*.
{info:title=User information is saved}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.{info}
The [AIM Template Manager|AIM Template Manager User's Guide] is a tool used to create an AIM template XML document.
!worddav4e10ff629ab31ef7129cc559ce2cbded.png|vspace=4, border=2, alt="AIM User Information dialog box"!
_Figure 8. AIM User Information_
h3. Detailed Description of a Question
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.
!worddav8637ba968963665d67cc71f8544166e1.png|vspace=4, border=2, alt="AIM Annotation dialog box showing pop-up window definition of a question"!
_Figure 9. Detail Description of a Question_
h3. AIM Locator
The AIM locator, depicted in (Figure 10), 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.
!worddav439c2ef3a8977ddafc101b3646020633.png|vspace=4, border=2, alt="AIM Locator showing available AIM annotations and a Show Study link"!
_Figure 10. AIM Locator_
h3. AIM Annotation Details
The AIM annotation details, as illustrated by Figure 11, 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.
!worddav2411cb98711e826e806fe6f7a80ca2d0.png|vspace=4, border=2, alt="AIM annotation details for a selected annotation"!
_Figure 11. AIM Details_
h3. AIM Display Markups from Different Users
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.
!worddav8021bf0972aab394b0ee79ca524c6bf8.png|vspace=4, border=2, alt="Visible AIM Users option is selected and three readers' names are listed next to it"!
_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 Figure 12. To assign a color to a user, go to *Tools* > *Options* > *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.
!worddav8508fdb6d19b3907479644e87b07692c.png|vspace=4, border=2, alt="AIM Markup display options"!
_Figure 13. AIM Markup Display_
h2. Viewing AIM Data for Each Image Series
You can see AIM annotations for an imaging study grouped by image series in the Available AIM Annotations section. Figure 14 shows two different image series. The first, Axial FSE, includes one AIM instance. The second, Axial T1, includes three AIM instances.
!worddav0d45f4cd1b5259267828d09947174490.png|vspace=4, border=2, alt="AIM Explorer showing the Available AIM Annotations pane, which lists two groupings of annotations. AXIAL FSE contains one annotation while AXIAL T1 contains three annotations."!
_Figure 14. AIM Data in Each Image Series_
h2. Using Data Services
h3. National Biomedical Imaging Archive (NBIA) Data Service
The NBIA Data Service (Figure 15) tab provides the ability to connect and retrieve studies from NBIA directly within the workstation. Holding the *Ctrl* key allows you to click on and select multiple studies. Right-clicking activates a feature that allows you to retrieve selected studies.
!worddavfe7d0a3ce2f75a5c8316e37a56a9a2a4.png|vspace=4, border=2, alt="Explorer window showing NBIA studies"!
_Figure 15. NBIA Data Service_
Users can enter search parameters (Figure 16) 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.
!worddavc7fd550051009b886912fad52c9b92be.png|vspace=4, border=2, alt="Search NBIA dialog box"!
_Figure 16. Search NBIA Data Service_
Columns in the NBIA Data Service page can be selected or deselected to display or hide an available result. Figure 15 depicts that all available columns for the service have been selected.
!worddav99a2db1da2a19b0b9ff976c0e09a020a.png|vspace=4, border=2, alt="List allowing you to select column options to display such as Patient ID, Sex, and DOB"!
_Figure 17. Select NBIA Data Service Display Columns_
h3. AIM Data Service
The AIM Data Service tab (Figure 18) provides the ability to connect and retrieve AIM XML documents from an AIM 3.0 Data Service (see [#Setting AIM Data Service Options]). It also allows a user to retrieve both AIM documents and studies from NCI's NBIA. Right-clicking activates a feature that allows you to retrieve studies.
!worddav65b0825029861188323bb71e6d4634d8.png|vspace=4, border=2, alt="Right-click menu offering Retrieve Selected Annotation option and Retrieve Selected Annotation and Study option"!
_Figure 18. AIM Data Service_
You can enter search parameters (Figure 19) based on a single value or multiple values of Anatomic Entities, Anatomic Entity Characteristics, the user who created the AIM XML documents, Imaging Observation, Imaging Observation Characteristics, and Study Instance UID.
{info:title=The AIM Data Service search is case-sensitive.}{info}
A type of AIM XML document, Imaging Annotation, or Annotation Of Annotation, must be selected. The default value is Imaging Annotation.
!worddav526d88050e33e5e0b43dc94334c515f5.png|vspace=4, border=2, alt="Search AIM Data Service dialog box"!
_Figure 19. Search AIM Data Service_
Columns in the AIM Data Service page can be selected or deselected to display or hide an available result. Figure 20 depicts that all available columns for the service have been selected.
!worddav049781f7e58e22048e9232c459b8dcb3.png|vspace=4, border=2, alt="List allowing you to select columns to display"!
_Figure 20. Select AIM Data Service Display Columns_
h2. Additional Information
Follow the links below for more information on how to set up AIM, information on the AIM Template Manager, and AIM Template Manager software.
* [AIM Terms and Concepts]
* [AIM Template Manager User's Guide]
* [AIM Template Software Setup manual|https://gforge.nci.nih.gov/frs/download.php/9167/AIMTemplateSoftwareSetup.zip]
* [AIM Template Creator Software|https://gforge.nci.nih.gov/frs/download.php/9166/template_editor.war]
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