Troubleshooting

Common Access Issues

Cannot Access Fileglancer

Symptoms: Fileglancer page won’t load or shows connection errors

Possible Causes & Solutions:

Network connectivity

• Check: Verify you’re connected to the Janelia internal network
• Solution: Connect to Janelia VPN if working remotely
• Test: Try accessing other internal Janelia resources

Site maintenance or server down

• Check: A maintenance or server down warning will appear
• Solution: Try accessing the site later
• Contact: Reach out on the #fileglancer-support Slack channel if not resolved

Authentication issues

• Check: Ensure your Janelia credentials are current
• Solution: Log out and log back in to refresh authentication
• Contact: Reach out to IT if password reset is needed

File System Access Problems

Symptoms: Can’t see expected directories or get permission errors

Possible Causes & Solutions:

1. POSIX permissions
   • Check: Verify you have appropriate permissions for target directories
   • Solution: Contact your system administrator
   • Group access: Ensure you’re in the correct user groups

Navigation and Browsing Issues

Slow or Unresponsive Interface

Symptoms: Pages load slowly, interface feels sluggish, or operations timeout

Possible Causes & Solutions:

Large directory handling

• Issue: Directory contains thousands of files
• Solution: Navigate to more specific subdirectories
• Report: Open a ticket in Clickup or reach out on #fileglancer-support

Network latency

• Issue: Slow connection to file systems
• Check: Test other network-intensive operations
• Try: Close unnecessary tabs and applications
• Report: Contact IT if consistently slow across all operations

Missing Files or Directories

Symptoms: Expected files don’t appear in directory listings

Possible Causes & Solutions:

Permission restrictions

• Issue: Files exist but you lack read permissions
• Solution: Contact data owner or system administrator

Hidden files

• Issue: Files are hidden by default (Unix hidden files starting with ’.’)
• Solution: Look for view options to show hidden files
• Alternative: Use direct path navigation if you know the filename

File system synchronization

• Issue: Recent files haven’t synchronized across file systems
• Solution: Refresh the directory view
• Verify: Check the original location where files were created

Data Links Not Working for Collaborators

Symptoms: Data links work for you but not for others

Possible Causes & Solutions:

Network access

• Issue: Collaborators not on Janelia network
• Solution: Ensure they’re connected to VPN or internal network
• Alternative: Consider setting up a data_external folder to share the data

File Conversion Issues

Symptoms: Conversion requests don’t submit or fail processing

Possible Causes & Solutions:

Incomplete request information

• Issue: Missing required fields in conversion request
• Solution: Review and complete all required form fields

Source data accessibility

• Issue: Technical staff can’t access source data
• Verify: Double-check source data paths in request

Scientific Imaging Format Issues

Zarr/OME-Zarr Problems

Symptoms: Zarr datasets won’t open or display incorrectly

Possible Causes & Solutions:

Incomplete Zarr structure

• Issue: Missing .zarray or .zattrs files
• Solution: Avoid modifying Zarr directory structure manually
• Recovery: Contact technical staff for structure repair

Corrupted chunks

• Issue: Individual chunk files are corrupted
• Solution: Request data validation and repair
• Prevention: Avoid interrupting write operations to Zarr datasets

Metadata inconsistencies

• Issue: OME metadata doesn’t match actual data structure
• Solution: Request metadata validation and correction
• Tools: Use OME-Zarr validation tools if available

Data Viewer Integration Issues

External Viewer Problems

Symptoms: Data viewers (Neuroglancer, Vol-E, Avivator) won’t open or display data incorrectly

Possible Causes & Solutions:

Data format compatibility

• Issue: Dataset format not supported by selected viewer
• Solution: Try a different viewer or request data conversion
• Check: Use OME-ZARR Validator to verify dataset compliance

Data link accessibility

• Issue: Viewer can’t access data through Fileglancer data link
• Solution: Verify data link is active and accessible
• Test: Try accessing the data link URL directly in browser

Viewer loading failures

• Issue: External viewer opens but shows blank screen or errors
• Solution: Check browser console for error messages, share with Fileglancer team
• Alternative: Try opening dataset with a different viewer

Metadata or scaling issues

• Issue: Data loads but appears incorrectly scaled or oriented
• Solution: Verify OME metadata is complete and correct
• Request: Contact technical staff for metadata validation
• Workaround: Use viewer controls to adjust display settings

Getting Additional Help

To get additional support:

• Reach out on the #fileglancer-support Slack channel
• Fill out the Clickup issue form