This tutorial guides you through the file conversion process.

Supported File Formats

  • Single 3D image stack (single-channel or multi-channel)
  • .tif / .tiff files, assumed in ZCYX order
    (this is the typical layout exported by ImageJ)
  • uncompressed .nii files

Files will be converted into the large-scale compatible
SISF format, optimized for efficient online visualization and annotation.

Steps

  1. Go to Raw File Management.
  2. Click Actions next to the uploaded file.
  3. Select Convert to SISF.
  4. Confirm that the Globus upload has fully completed in the Globus window.
    If confirmed, click Yes, Continue.
  5. Enter metadata for the file:
  6. Number of channels
  7. Physical resolution (XYZ)
  8. Image size (XYZ)
  9. Click Start Conversion.
  10. Once conversion completes, the field SISF Conversion? will show Yes.
  11. (Optional) Click Add to SISF Library to add the dataset to the SISF Image Library.

Progress Monitoring

  • Navigate to Jobs to track conversion progress.
  • You may cancel the job if needed.

Troubleshooting

  • If the job status shows Failure:
  • Confirm that all metadata matches the actual file.
  • View metadata under Actions → View Details on the Jobs page.
  • Common issues include:
    • Image size mismatch
    • Channel number mismatch

If issues persist, contact the site administrator for assistance.