File Conversion Requests

Fileglancer integrates with Janelia’s JIRA help desk system to handle manual data conversions. This feature allows you to request assistance converting your scientific imaging data between different formats.

Supported Source Formats

Fileglancer conversion requests typically support:

Zarr arrays: Existing Zarr datasets that need reformatting
OME-Zarr: Conversion between OME-Zarr versions or structures
TIFF files: TIFF data conversion to OME-Zarr format
OME-TIFF: Metadata-rich TIFF conversions

Requesting File Conversions

Prerequisites

Before requesting a conversion:

Verify source data accessibility

Ensure you can navigate to and view the source data in Fileglancer
Confirm the data is complete and not corrupted
Check that you have read permissions for the source data

Determine target format requirements

Know what format you need for your analysis workflow
Understand any specific parameters or options required
Consider where the converted data should be stored

Prepare conversion details

Document any special requirements or constraints
Note any metadata that must be preserved

Step-by-Step Conversion Request

For Zarr and OME-Zarr Data

Navigate to your Zarr directory
Use any navigation method to reach the Zarr or OME-Zarr directory. Ensure you’re at the correct directory level containing the data.
Open the Properties Panel
Locate the Properties Panel on the right side. If not visible, look for the expand Properties button in the browser toolbar, on the right.
Switch to the Conversion tab
Click on the “Conversion” tab within the Properties Panel.
Open the conversion request
Click the button to “Open conversion request”. This will open a dialog.
Complete the dialog
Fill out the dialog with required information.
Submit your request
Submit the dialog. View the information about the ticket now populated in the Properties panel.

Screenshot of the Fileglancer interface, with an arrow pointing to the Conversion tab in the Properties panel on the right side of the screen, and the button in the Conversion tab to open the file conversion dialog.

Tracking Your Conversion Requests

Using the Tasks Page

Navigate to the Tasks page
Click on the Tasks page link at the top of the interface.
View your requests
See all current conversion requests and their status. Monitor progress through different conversion stages.

Screenshot of the Tasks page on Fileglancer interface, showing the table with created tasks.

Status Meanings

Understanding conversion request statuses:

Submitted: Request received and queued for processing
In Review: Technical staff reviewing the request details
In Progress: Conversion actively being performed
Completed: Conversion finished and data available
On Hold: Waiting for additional information or clarification
Failed: Conversion encountered errors (details provided)

Accessing Converted Data

Check completion notification
Monitor the Tasks page for completion status. Look for email notifications as well.
Locate converted data
Navigate to the specified output directory. Verify the converted data is accessible.
Validate conversion results
Check that the converted data opens properly in your analysis tools. Verify metadata preservation. Compare file sizes and structure as expected.

Troubleshooting Conversion Issues

Common Request Problems

Problem: Conversion request form won’t submit

Solution: Check that all required fields are completed
Verify you’re still authenticated to the system
Try using a different browser if issues persist

Problem: Can’t find the Conversion tab

Solution: Ensure you’re navigating to Zarr or OME-Zarr directories
Check that the Properties Panel is fully expanded
Verify you have appropriate permissions for the directory

Conversion Process Issues

Problem: Conversion failed or produced unexpected results

Solution: Contact technical staff through the help desk system
Provide specific details about what you expected vs. what occurred
Include sample files or detailed error descriptions

Problem: Converted data is missing metadata

Solution: Review your original conversion request for metadata requirements
Contact technical staff to clarify metadata preservation options
Consider requesting a re-conversion with specific metadata instructions

Problem: Conversion taking longer than expected

Solution: Check the Tasks page for status updates
Contact technical staff if no progress updates are visible
Consider if the dataset size or complexity requires additional processing time

The file conversion system in Fileglancer provides professional data conversion services while maintaining the integrity and accessibility of your scientific imaging data. Use it as a reliable way to prepare your data for analysis, sharing, and long-term preservation.