RDCRN Ambra User Guide

Owned by Michael Wagner
Last updated: Dec 13, 2024 by Joshua Fortriede
7 min read

Login

The login URL for Ambra is ambra.rdcrn.org. The Tool Garden accessible from the members landing page now contains Ambra. Once Ambra is setup for a protocol, it will also appear on the Protocol Resources page for that consortium.

2-Factor Authentication

Because Ambra can contain PHI, login requires the use of the RDCRN 2-Factor Authentication setup. If you have already set this up for other RDCRN applications such as Box or Redcap, nothing else should need done. To setup the 2-factor authentication, follow our instructions here.

Uploading Images

The basic steps to uploading images are: selecting the location to store the uploaded image(s), selecting the folder containing the image(s) to upload, inputting metadata for the images such as participant IDs or visit name, and then uploading the images. These steps are described below.

  1. Choose the location where the uploaded images will be uploaded, click “Upload Images”, and then select “Upload Studies”.

     

     

  2. Click “Select DICOM folder” to select the folder that contains the imaging files to upload. You will then receive a prompt stating how many files will be uploaded, and it will ask you to “Upload” or “Cancel”. Click “Upload” to continue. There may or may not be a checkbox to “Select files for DICOM wrapping”. Use this feature only if you are uploading photos (jpgs, pngs, etc) and not if you are using normal DICOM files.

    1. Note: When you are uploading DICOMs, you will be selecting a folder and not individual files. The selected folder and sub-folders will be scanned for any DICOM files.

       

       

  3. After scanning the files, a table will appear that summarizes the image files. Each row represents an individual series in an Imaging Study, and provides general information about that series; including the series description, number of images, modality type, study date, and patient’s name and DOB. Series can be unchecked to remove them from the upload process.

     

     

  4. Below the table are a series of fields that need to be filled out. These fields will vary depending on the protocol, including if they are already pre-filled or not. Required fields will have an asterisk “*” preceding the field label. The values in these fields are associated with each study/series that is uploaded. To selectively change a field value for an individual series, click the edit button next to the series.

  5. If the images contain pixels that need to be removed (such as Dose Reports, or embedded PDFs), this can be done prior to upload or once the images are within Ambra. To mask pixels prior to upload click the “Use DICOM pixel de-identifier before upload” button.

  6. Once all fields are filled out, click “Upload Selected Studies”. Upload progress is displayed, and you will see a notification of when all images have been uploaded.

     

     

Approve Images

Protocols are setup so that images uploaded to the clinical sites require approval within Ambra to be fully stored and shared outside of the clinical site space. This approval also finishes the DICOM tag based de-identification process.

Any images uploaded after December 13th, 2024 will require the images to be VIEWED prior to approval.

  1. After images are uploaded, they will go into an approval queue. This queue can be accessed by clicking on the “Activities” link in the top toolbar.

     

  2. Study/Image metadata can be viewed and edited by clicking on the “Edit” button.

  3. Images can be viewed by clicking on the “Images” button. To redact pixels from the image, see Pixel-Based Redaction.

  4. Within the activities view, you can view images, edit the metadata associated with the imaging studies, and approve or reject the images. 

Image De-identification

There are two types of image de-identification: DICOM tag based, and Pixel based. DICOM tag de-identification is setup to occur automatically, while pixel-based de-identification is a manual process.

DICOM tag Removal/Anonymization

PHI containing DICOM tags are removed on upload/after approval. These tags were identified by the DICOM standards committee of the National Electrical Manufacturers Association (NEMA), in their DICOM attribute confidentiality profiles section. A complete list of our implementation of these standards and the affected DICOM tags is forthcoming. In addition, all “Private Tags” are removed as these can also contain PHI.

Pixel-Based Redaction

  1. Within the Ambra ProViewer, image pixels can be redacted on the image, series, or study level. To redact pixels, click on the Redact item in the toolbar and then choose whether you want to redact pixels from the current image, the current series, or the entire study. If you do not see the “Redact” icon in the toolbar, please see “Configuring Ambra ProViewer”.

     

     

  2. Once selected, draw the region of which you would like to redact. Multiple regions can be drawn.

  3. After all regions are drawn, click the “Redact” toolbar item and then click “Redact All Regions”. A prompt will ask you to confirm the redaction.

Configuring Ambra ProViewer

The Ambra ProViewer can be configured by clicking the “Settings” icon in the toolbar.

 

Enable Image Pixel Redaction

To ensure that pixels can be redacted from the current image, series, or study, follow these steps.

  1. If the “Redact” icon is not present in the toolbar, click on the “Settings” Icon, then select “Toolbar” from the left-sided menu.

  2. Under “Available Tools”, scroll down to the “Quality Control” section, locate the “Redact” icon, and drag it into the “Toolbar” column in the position you want it to appear.

  3. Click back to the “General” tab and scroll down to the “Editing” section.

  4. Make sure the “Edit Current Study (No Copy)” checkbox is checked.

  5. Click “Save All” in the bottom left of the screen.

 

Enable Volumetric Measurements

Volumetric measurements can be done by making “traces” on sequential slices of certain images.

To enable:

  1. Click on the “Settings” icon

  2. In the “General” tab, under “Annotations”, check the checkbox “Enable Volume Measurements”

  3. Click “Save”

  4. Click on the Toolbar tab.

  5. Under “Available Tools”, find “Trace” in the Annotation section and drag it into the toolbar column in the order you would like it.

  6. Click “Save”

To use:

Select the “Trace” tool, and trace overlapping regions on sequential slices. Once sequential, overlapping traces are established, a volume measurement will appear in the trace statistics.

 

 

Customizing Ambra per User

Ambra accounts can be customized in various ways to enhance a user’s experience. These customizations include event notifications, default pages, and myriad settings within the ProViewer.

Setting up Event Notifications

Notifications can be turned on to email users when certain events occur. These events include, but are not limited to, image upload, image share, image status change, and image upload failures.

  1. Click on your name in the upper right corner of any page.

  2. Next, click on the “Notifications” link.

     

     

  3. Select the notification type (columns) that you want to turn on/off for the given Ambra workspace (rows).

     

     

  4. After selecting/deselected the desired notifications, click the “Save” button in the bottom left of the page.

Configure ProViewer

ProViewer configuration and usage instructions can be found in the Ambra ProViewer Guide.

 

Creating Reports

Users are able to create reports in Ambra in all of the name spaces in which they have access. To create a report, click “detail report” at the bottom right hand corner of the screen.

Upon clicking “detail report,” a box will appear to select which variables the report should show. One all columns are selected, an Excel file of the report will download.

Helpful fields to select could include:

  • Modality - which shows the image type (i.e. CT, MR, OT). NOTE: OT likely means the images is a WRAPPED DICOM file.

  • image_count - number of total images from all studies

  • clinical_site - site in which images were uploaded

  • Consortia - count of the numbers of studies for a particular study

  • protocol_id - RDCRN protocol number in which images were uploaded

  • global_local_ID - listing of the local IDs that have imaging studies uploaded

To see the report data in tabular format, create a Pivot table in Excel.

To create a report of number of studies by site in a particular study, complete the following steps:

  • Select all columns in the Excel report

  • Navigate to the Insert tab, then select Pivot Table

  • Select “clinical_site” for the rows and “Consortia” for the values

Support

The support page can be accessed by clicking the “Help” link in the upper portion of the page.

If you are unable to log into the Ambra platform or experience slowness or other oddities, please check the Ambra status page to see whether there is an issue with Ambra itself.

Submitting tickets to the RDCRN Helpdesk

To submit a ticket to the RDCRN Helpdesk system, click on the “RDCRN Helpdesk” link.

Frequently Asked Questions (FAQ)

Answers to commonly asked questions can be found in our FAQ section.