De-identification

How to Remove Labels and Patient Data from Slide Images

A whole-slide image carries more than the tissue: a photo of the slide label, an overview photo that often shows the label too, a file name that may hold the case number, and metadata such as barcodes, dates and scanner details. Before sharing a slide, remove all of them, without touching the pixels you want to share. Here is what to remove, and the tools that do it.

Download SlideScopeCompare the tools
Label, overview, file name, metadataPixels unchangedDone on your computer

What identifies a slide file

  • The label image: scanners store a photo of the slide label, often with a name, case number or barcode.
  • The overview (macro) photo: a picture of the whole glass slide, which usually shows the label as well. On some NDPI and Ventana files the label and overview are one image.
  • The file name: often the case or accession number.
  • Metadata: decoded barcodes, label text read by the scanner, acquisition dates and times, the scanner serial number and operating-system user names.
  • The image itself: a label or handwriting caught inside the scanned area is part of the pixels and no tool removes it without editing the image.

Source: the wsi-anon paper (PMC10185865); OpenSlide associated images and properties.

Tools that de-identify slides

ToolCostFormatsWhat it does
SlideScope “Save a Safe Copy”Paid; comes with the 3-day free trialSVS, NDPI, BIF, QPTIFF, AVS, OME-TIFF and tiled TIFF, CZI, single-file DICOMRemoves the label and overview photos and identifying fields, drops the file name, leaves pixels byte-for-byte, then checks the copy; refuses MRXS, SCN, VMS/VMU, VSI
svs-deidentifierFree (MIT)Aperio SVSStrips the label and macro images; copy or modify mode; desktop app for Windows, Mac and Linux
wsi-anon (EMPAIA)Free (MIT)MRXS, NDPI, SVS/TIFF, iSyntax, BIFC library with Python and JavaScript bindings; for pipelines
anonymize-slideFree (GPL-2)SVS (label only), NDPI (macro), MRXS (barcode)Edits the file in place; Python 2; last changed in 2015
DICOM de-identification profileStandardDICOM WSIBasic Profile plus the Clean Pixel Data option for burned-in text

Tools that edit the original in place leave you no untouched copy if something goes wrong: work on a copy, and keep the original under its access controls.

How to save a de-identified copy in SlideScope

  1. Open the slide in SlideScope on Windows or Mac.
  2. Choose File › Save a Safe Copy… and pick where to save it.
  3. SlideScope writes a copy without the slide label and overview photos and the identifying fields stored in the file, under a new name, with the image data left byte-for-byte as it was. It then checks the copy independently; if the check fails, the copy is deleted and nothing is called safe.
  4. Look over the copy for anything inside the scanned area, such as handwriting on the glass, which no tool can see.

File › Remove Identifying Details from Exports also keeps the original file name out of exported images, and share links can use the same clean copy. Safe copies come with the 3-day free trial or a subscription.

Checklist before you share a slide

  1. Work on a copy, never the original.
  2. Remove the label image and the overview photo.
  3. Remove identifying metadata: barcode, label text, dates, scanner and user details.
  4. Rename the file so it does not carry a case number.
  5. Check the scanned area itself for writing.
  6. Confirm what your institution and ethics approval allow you to share.

De-identification questions

Does removing the label image make a slide anonymous?

Not on its own. The overview (macro) photo often shows the label too, the file name may carry the case number, and the file’s metadata can hold a barcode, label text, dates, the scanner serial number and user names. Writing caught inside the scanned area is part of the image and stays.

Can I remove the label from an MRXS or VSI slide?

Some tools handle MRXS (wsi-anon removes the slide barcode level), but these multi-file formats are harder to clean safely. SlideScope refuses to call an MRXS, SCN, VMS/VMU or VSI copy safe rather than guess.

Does de-identifying change the image pixels?

It should not. SlideScope’s safe copy leaves the image data byte-for-byte as it was (nothing is re-encoded), so annotations and measurements still line up, and it verifies the copy before calling it safe.

Is de-identification enough to share patient slides?

It is one step. What you may share, and with whom, is set by your institution, ethics approval and data-protection rules; check with them. This page is practical guidance, not legal advice.

Is SlideScope free?

SlideScope is a paid app with a free preview (open, measure and annotate a few of your own images) and a 3-day free trial.

Free preview: open, measure and annotate up to 5 of your own images. No account or card needed. Export, sharing, comparing slides and AI Analysis come with the 3-day free trial: $0 today, then $25/month unless you cancel before it ends. PayPal or card required, and you can cancel anytime from your account. Annual billing is available at $249.99/year, which works out to about two months free.

Share slides without the label

Open your own slides with the free preview, then save safe copies with the 3-day free trial. Already decided? Subscribe now.

Download SlideScope