User Guide

This guide will help you get started with using BrainMaps for your research.

Browsing Brain Data

Categories and Species

1. From the homepage, you’ll see different categories of animals (Ants, Birds, Cephalopods, etc.)
2. Click on a category to see all species within that group
3. Select a species to view available brain scans

Viewing Brain Details

When viewing a brain scan, you’ll find:

• High-resolution images
• Upload date and contributor information
• Verification status
• Unique readable ID
• Reference images (if available)
• Visualization options

Visualizing Brain Data

Using the Visualizer

1. Click the “Visualize Brain” button on any brain entry
2. The visualizer supports multiple formats:
   • TIFF files: Standard image stack format
   • Zarr files: Optimized for large datasets
   • NIfTI files: Neuroimaging format (automatically converted)

Visualization Features

• Pan and zoom through the brain structure
• Adjust contrast and brightness
• View in different planes (sagittal, coronal, axial)
• Direct link to visualization URL
• Support for both local and cloud-hosted files

Uploading Your Data

Supported File Formats

• .nii - NIfTI format
• .nii.gz - Compressed NIfTI
• .zarr - Zarr format
• .tif/.tiff - TIFF format

Preparing Your Files

Before uploading, ensure your data is:

• In a supported format
• Properly oriented and aligned
• Includes relevant metadata
• Within size limits for your account

Upload Process

1. Click “Upload” in the navigation bar
2. Select your file(s)
3. Fill in required information:
   • Name (descriptive title)
   • Species association
   • Description
   • Reference images (optional)
4. Wait for processing:
   • File validation
   • Cloud storage upload
   • Format conversion (if needed)
   • Metadata extraction

Upload Status

Your upload will go through several stages:

• uploaded: Initial file upload complete
• processing: File being processed/converted
• completed: Ready for viewing
• failed: Error occurred (check error message)

After Upload

• Your data will be marked as “Unverified” initially
• Platform administrators will review the submission
• Once verified, it becomes publicly accessible
• You can track the status in your uploads dashboard

Account Management

Profile Settings

• Update your personal information
• Change email preferences
• Manage your uploads
• View usage statistics

Data Management

• View your uploaded brains
• Track verification status
• Update metadata
• Remove outdated data

Best Practices

Data Quality

• Use consistent orientation for all scans
• Include clear descriptions
• Add reference images when possible
• Verify metadata accuracy

Sharing Data

• Use unique, descriptive names
• Include detailed descriptions
• Tag collaborators
• Share direct links

Getting Help

Common Issues

• File upload problems
• Visualization errors
• Account access issues
• Data management questions

Support Resources

• Check the FAQ section
• Contact support
• Join the community forum
• Report technical issues

Privacy and Data Usage

Data Visibility

• All uploaded data is public by default
• Users can see who uploaded each brain
• Download statistics are tracked
• Usage analytics are available

Citations and Attribution

• How to cite BrainMaps in your research
• Proper attribution for specific datasets
• Licensing information
• Usage guidelines

Advanced Features

API Access

• Available for programmatic access
• Requires authentication
• Suitable for batch operations
• Documentation available

Batch Operations

• Upload multiple files
• Download datasets
• Update metadata
• Generate reports

Updates and Changes

Stay informed about:

• New features
• Platform improvements
• Maintenance schedules
• Community updates

Contributing

Help improve BrainMaps:

• Report bugs
• Suggest features
• Share feedback
• Contribute documentation