This tutorial guides the process for using nnInteractive for AI-assisted image annotation.

First-time Usage

nnInteractive runs in a separate environment.
Please contact the site administrator to set up your account before first use.

Ignore the "Authenticate" window and close it.

Prepare ROI Image Data

  1. Open an image dataset and select an ROI
    (refer to the Basic Operations Guide).
  2. In the ROI Selection dialog, click Annotate.
    This will download the ROI image data to your nnInteractive workspace.

Annotate

  1. Click nnInteractive in Quick Access and log in with your credentials.
  2. Your ROI data will appear in the data folder on your desktop.
    This folder is protected, meaning you cannot modify or delete files directly inside it.
  3. To work on a file:
  4. Create a new folder on your desktop
  5. Drag the desired ROI file from the data folder into your new folder
  6. Perform annotation on the copied file

This process ensures the original ROI dataset remains intact.

For instructions on how to use nnInteractive tools, see the nnInteractive documentation.

Continue Saved Segmentation

  1. Open the image and initialize it
  2. Open the autosaved segmentation, select it
  3. Click Load Previous Instances on the right
  4. Continue your work

It is definetly frustrated if the noVNC disconnects or napari just crashs. But we now can continue previous work, with some loss :( though. The segmentation will be saved automatically every 15 minutes.

Load Previous Object

  1. Change the class ID to that object's ID on the right panel
  2. Click Load Single Objecton the right panel
  3. Continue working on that object as you usually do

Troubleshooting

  • I do not see the nnInteractive option in Quick Access

    • Your account may not be activated yet
    • Contact the site administrator

  • I cannot log in

    • Ensure your nnInteractive account has been created
    • Try resetting your credentials if applicable

  • My ROI file is not appearing in the data folder

    • Confirm the ROI selection was downloaded (click Annotate again)
    • Check that the upload/conversion job has completed in the portal
    • Restart nnInteractive and refresh the folder view

  • I cannot delete or move files inside data

    • This is expected — the folder is protected
    • Copy files to a new workspace folder instead

  • Annotation changes are not saved

    • Ensure you are editing files in your own folder, not data
    • Confirm local disk permissions are not restricted

  • Viewer loads but image is blank

    • Try re-opening the file
    • If the problem persists, the ROI conversion may have failed — contact the administrator