Annotate Images

The V3 viewer comes with a series of tools that allow you to create annotations. These annotations can be saved to Flywheel and be re-loaded in the viewer for further review and analysis.

Create annotations

Create an annotation

1. In the Viewer, select a tool from the Measure Tools menu in the right-side toolbar.

   

1. Depending on which tool you chose, draw an annotation on the image. Once you are done drawing, the Measurements panel will automatically open and your annotation will be listed there.

   

2. Additional annotations can be created on different slices of the same image file. Clicking on an annotation in the measurement panel automatically displays that annotation in the viewport.

3. Additional annotations can be created on different image files. Annotations are then grouped by image file in the measurement panel.

   

Create a new measurement set

By default, annotations created on a single image file are grouped together as a "measurement set" so that they can be saved together. In some cases, one might want to create a separate measurement set to avoid making changes to an existing set, or one may want to compare measurement sets from two different users.

To create a new measurement set for a specific image file, click on the "Add measurement set" icon next to the "Save measurements" button for the active measurement set in the measurement panel.

When multiple measurements sets are opened in the measurement panel for the same image file, newly created measurements are added to the active measurement set.

Each measurement set can be saved separately (see Save measurements).

Tools

The following tools are available by default in the viewer:

Annotation

• Annotation tool: Adds an arrow to the image with custom text (label) as annotation. Label is required.

Measurements

• Length tool: Measures the length between two points on an image. Length is displayed in mm if images have the Pixel Spacing (0028,0030) tag. It is displayed pixels (px) otherwise.
• Bi-directional tool: Measures the width and length of a structure on an image by drawing two perpendicular lines. Length and Width are displayed in mm if images have the Pixel Spacing (0028,0030) tag. It is displayed in pixels (px) otherwise.
• Angle tool: Measures the angle formed by three points on the image.
• Freehand tool (open contour): Measures the length of a freehand-drawn contour. Length is displayed in mm if images have the Pixel Spacing (0028,0030) tag. It is displayed pixels (px) otherwise.

ROIs

• Circle ROI: Measures the radius, area, and pixel intensity statistics (mean, max, standard deviation) of a circle region of interest.
• Ellipse ROI: Measures the area and pixel intensity statistics (mean, max, standard deviation) of an elliptical region of interest.
• Rectangle ROI: Measures the area and pixel intensity statistics (mean, max, standard deviation) of an rectangular region of interest.
• Freehand tool (closed contour): Measures the area and perimeter of a freehand-drawn region of interest.

Undo/redo

The "undo" button can be used to correct any mistake made while drawing annotation or to cancel the creation of an annotation. When no edits are made following an "undo", the "redo" button can be used to revert the "undo" action.

Save annotations

Annotations made on one image file can be saved as a measurement set in Flywheel by clicking the Save Measurements > Save As... in the measurement panel.

Enter a name for the measurement set. If it's the first time measurements are being saved, the name is pre-populated with the Flywheel acquisition name of the related image file. Name is limited to 100 characters.

Upon saving, the measurement set is added as an overlay for the related image file in the left-side panel. See also Load from a saved measurement set

Each time a measurement set gets saved under the same name, it creates a new version of that measurement set.

Annotations Quick View in Flywheel

When an image file has saved measurement sets, an annotations quick view icon is visible at the file level in Flywheel. The icon also has a badge with a count of the number of saved measurements sets for the image file.

Clicking on the annotations quick view icon displays a summary of all the measurements sets saved for that image file. For each measurements set, the annotations quick view provides the following information:

• Name of the measurement set
• User who saved the measurement set
• Date and time the measurement set was saved
• Number of measurements saved in the measurement set
• Summary of measurements grouped by label

For each label, the annotations quick view provides the number of annotations grouped under that label (see also Group measurements by label) and the total area if there are one or more area measurements under that label. If a saved measurement set contains measurements without a label, those are marked as Unlabeled in the annotations quick view.

Load annotations

Load from a saved measurement set

Saved measurements sets can be loaded back into the viewer for review or editing. When an image file has saved measurements sets, an Overlays menu is available from that image file thumbnail in the left side panel of the viewer.

To load a measurement set in the viewer, select it in overlays menu and click "Load". The annotations will be opened in the measurements panel and the associated image file will be loaded into the active viewport (if not already loaded). Multiple measurements sets can be selected an loaded simultaneously. Once a measurement set is loaded, it can no longer be selected from the overlays menu.

Load from a DICOM Structured Report

If annotations were saved previously as DICOM Structured Report, they can be loaded in the viewer through the left-side panel file browser (see Load more files from the same acquistion). Simply load the DICOM Structured report into the left-side panel and drag and drop it into a viewport. Measurements will be restored in the measurement panel under the same measurement set.

Label annotations

Labels can be assigned to annotations to indicate what they represent. Depending on the viewer's configuration, the user experience to assign labels will differ.

Assign a label to a new measurement

Without label prompt (default)

When the viewer is configured with labelOnMeasure set to false, users are not prompted to enter a label upon creating a measurement. By default the measurement is created without a label and is stacked at the bottom of the list of measurements from the active measurement set.

To assign a label to an unlabeled measurement see Edit the label of an existing measurement

With label prompt

When the viewer is configured with labelOnMeasure set to true, users are prompted to enter a label upon creating a measurement. The options available in that prompt vary based on additional configuration (e.g. pre-defined list of labels, ability to create new labels, etc...)

Edit the label of an existing measurement

The label of a measurement can be edited by clicking on the Edit Label icon in the measurement panel, or by using the right-click menu while the measurement is active in the viewport.

From the measurement panel:

From the context menu on right-click:

Depending on the viewer’s configuration for the project you can type in a label and/or select a label from a pre-defined list. If a pre-defined list of labels exists you can start typing the name of a label from that list to quickly find it.

Group annotations by label

A single feature of the image may require multiple annotations (e.g. multiple closed freehand regions) to be fully captured. In that case, annotations can be assigned to the same label in order to be grouped together in the measurement panel. Grouped annotations are displayed with the same color, which is unique to each label.

When multiple ROIS are grouped under the same label, the sum of their areas (Total Area) is provided in the measurement panel. The total area does not account for potential overlapping ROIs. Other metrics like length or angle are not aggregated when grouping measurements.

Map to active label option

When multiple measurements need to be created with the same label, it can be tedious to have to assign the label to each individual measurement. Turning on the Map to active label option in the Measurements panel settings automatically applies the active label to newly created measurements.

Edit the color of a label

Upon creating measurements and assigning a label, each label is automatically assigned a random color. The color of a label can be edited by clicking on the color strip next to the label name in the measurement panel. All measurements grouped under that label will be assigned the new color.

Hide annotations

Annotations can be hidden by clicking on the Hide icon in the measurement panel or by using the right-click menu while the measurement is active in the viewport. When a measurement is hidden it is no longer displayed on the image. The label of a hidden measurement can still be edited.

From the measurement panel:

From the context menu on right-click:

Lock annotations

Annotations, measurements and ROIs can be locked to avoid accidentally editing them. This can be done from the measurement panel or by using the right-click menu while the measurement is active in the viewport. When a measurement is locked, it cannot be edited or deleted.

From the measurement panel:

From the context menu on right-click:

Delete annotations

Annotations, measurements and ROIs can be deleted from the image with the delete icon in the measurement panel or by using the right-click menu while the measurement is active in the viewport. Deleting a measurement removes it from the image and from the measurement panel. Deleting a measurement cannot be undone.

From the measurement panel:

From the context menu on right-click:

Hide output values for annotations

Output values are displayed on the image by default for each measurement. These can be moved by clicking and dragging. However, if multiple measurements or ROIs need to be created on one image, output values can rapidly get in the way. You have the option to hide the output values for each individual measurement or ROI from the right-click menu while the measurement is active, green contour in the viewport.

You can also decide to hide output values for all measurements and ROIs from the Settings menu in the measurement panel. Note: this does not apply to annotations.

Export annotations

You can export a csv file containing information about your annotations, measurements and ROIs by clicking Export (.csv) in the Save Measurements menu at the bottom of the measurement panel.

The exported csv file contains one row per measurement and the following columns:

• PatientID: populated with the PatientID (0010,0020) value of the annotated DICOM series.

• PatientName: populated with the PatientName (0010,0020) value of the annotated DICOM series.

• StudyInstanceUID: populated with the StudyInstanceUID (0020,000D) value of the annotated DICOM series.

• SeriesInstanceUID: populated with the SeriesInstanceUID (0020,000E) value of the annotated DICOM series.

• SOPInstanceUID: populated with the SOPInstanceUID (0008,0018) value of the annotated DICOM series.

• Label: Label assigned to the annotation in the Viewer.

• AnnotationType: The tool that was used for this annotation.

• FrameofReferenceUID: populated with the FrameOfReferenceUID (0020,0052) value of the annotated DICOM series.

• points: points coordinates of the contour’s annotation on the image

• Length: the length value of the annotation (if applicable)

• Unit: the unit of length of the annotation (if applicable)

Close annotations

You can close measurements sets by clicking on the close icon at the top-right corner of the measurement set in the measurements panel or by selecting “Close” from the “Save Measurements” menu at the bottom of each measurement set. This will close the measurement set.

If you have unsaved measurements, you will see a warning asking you if you are sure that you want to close. Click Yes to continue without saving or Cancel to go back to the measurement panel and save your measurements.