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Techcyte: Bulk Scan Import Tool

I. Introduction

The Bulk Import Tool is a utility provided to Techcyte users as a way to upload scanned image files. This tool supports DICOM, SVS, and TIFF uploads with optional metadata de-identification. De-identification occurs on the user's machine - no data is uploaded to Techcyte until the final upload page.

II. Prerequisites

In order to use the Bulk Import Tool you'll need:

  • A Techcyte account with appropriate permission (Lab admin OR Lab user)
  • The "Bulk import tool" feature flag turned on

III. Step-by-Step Instructions

We'll need to: select the files you want to upload, optionally redact PHI, keep/remove overview/label images, upload, and assign to a case.

1. Visit the Bulk Import page

From your worklist view, select Bulk Import from the menu dropdown

2. Select your files

Click "Select files" or "Select DICOM directory" to select your files. (A test image can be found here: CMU Openslide Sample)

NOTE: Files are modified if you don't select "Direct Upload"

3. View loaded files

Your image file should show in the list with a thumbnail. Click next to review metadata

4. Review the metadata for any PHI

Some fields are critical for maintaining file integrity and are turned off by default. Click Auto redact to remove all fields that are unnecessary. Click Next at the bottom of the page.

5. Verify the images

From this page you can review and omit label/overview images contained in the file. By default, SVS label and overview are removed when converting to TIFF redaction and uploading.

6. Review before upload

Review your file tags/images before uploading, download redacted files, and remove files from upload candidates. Click Finalize when ready.

7. Upload

Click Start upload and wait for the upload to complete.

8. View your uploaded scan

Click the link icon next to your image to review your scan.

9. Correct any issues with the scan

If your file's MPP could not automatically be determined, review your scan details and enter it on the Regions tab. Click reprocess and Save

10. Assign to a case

At the top of the page click "scan details page". From this page, select "Search for case" and add to your case (If you don't have one, see creating a case).

Alternatively, the scan can be added to your case by visiting your worklist page, and selecting the scans view.

Select your image, click "Link to case", and select your case.

IV. Troubleshooting

  • DICOM files with base layers over 2GB in size may present issues for some browsers when attempting de-identification. Try zipping your file, and selecting "Direct upload" on the first bulk import page. NOTE: Do not upload any files containing PHI, verify offline.
  • Disabling thumbnails will result in faster load times, especially for SVS/TIFF files, verify they contain no pixel PHI.
  • For running algorithms in bulk as you import, see creating a case policy.

V. Conclusion

In a few steps we've uploaded a sample SVS file, and reviewed it on the scans page.