How to Use the Pixel De-identifier

If you need to load and view DICOM files, mask burned-in PHI, and save the modified DICOM files, you can use Ambra’s Pixel De-identifier. Please note that this is a permission that will need to be turned on for your user account. If you do not have the Pixel De-identifier as an option, please contact your system administrator.

First, you will need to select your study to upload to Ambra. Please see our video on “ How to Upload” about uploading studies. 

Once you select the file from your computer, Ambra will scan the file for DICOM images. Once it is finished scanning, enable the ‘Use Pixel De-Identifier before upload’ checkbox, then click ‘Upload Selected Studies.’


The Pixel De-Identifier will display. Here, image data is displayed one series at a time. Use the scroll bar under the image to move to a different image.


To draw a mask, click and drag on the image.


If there are multiframe images in the series, a newly drawn mask covers all frames in the displayed file; otherwise, a new mask covers all images in the current series. To resize a mask, click the line handle on any corner and drag your mouse to the desired point. To move a mask, click in the center of the mask and drag your mouse to the desired area. To change the scope of a mask, click the gray button in the center of the mask.

A popup menu appears that allows you to delete the mask, or to set it to apply to all files in the current study (“Study”), series (“Series”), to all frames in the current file (“File”), or to only the current frame (“Frame”). Note that "File' and "Frame" are only different if the current file is multiframe. You can also select whether the edit should apply to the current series ("Series") or only the current frame ("Frame"). 


When you have finished drawing masks on the current series, click ‘Next Series.’

Click the ‘Upload with Changes’ button when you are done de-identifying your image. The Pixel De-Identifier will close and your study will be uploaded to Ambra.

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