Nutil: Neuroscience Image Processing and Analysis Utilities

Nutil documentation

• Introduction
• Technical information
• Conditions of use
• Release notes
  • Nutil v0.8.0
  • Nutil v0.7.0
  • Nutil v0.6.0
  • Nutil v0.5.0
  • Nutil 0.403
  • Nutil 0.402
  • Nutil 0.4.01
  • Nutil 0.4
  • Nutil 0.33
• Quality assurance / validation
  • Validation
  • Automated validation
  • Feature testing status
• Nutil as a command line tool
• Contact us

Pre-processing operations

• 1. TiffCreator
• 2. Transform
• 3. Resize

Quantifier operation

• 1. Introduction
• 2. Preparing the input files
  • 2.1. File naming requirement
  • 2.2. Preparing the Segmentations
  • 2.3. Preparing the Atlas Maps
  • 2.4. Preparing the XML or JSON file
• 3. How to run Quantifier
  • 3.1. Python plots
• 4. Object splitting explained
• 5. Custom masks explained
  • 5.1. QuickMask application
• 6. Customised reports explained
  • 6.1. CustomRegion reports
• 7. How to interpret the results
  • 7.1. RefAtlasRegion report
  • 7.2. CustomRegion report
  • 7.3. Object report
  • 7.4. Overlay images
  • 7.5. Coordinates
  • 7.6. NUT file
• 8. Warnings and error messages
  • 8.1. Quantifier
  • 8.2. Transform
• 9. FAQ
  • 9.1. I can’t open the application. “Windows protected your PC”
  • 9.2. Nutil shuts down during a run and/or generates corrupt files
  • 9.3. There are no object counts in the reports (N/A)?
  • 9.4. The reports (CSV) don’t open correctly in Microsoft Excel
  • 9.5. I don’t understand what to enter for the Pixel Scale?
  • 9.6. How do I calculate the Pixel Scale of images that have been downscaled?
  • 9.7. The QUINT coordinates do not match the Allen CCFv3. What’s going on?
  • 9.8. The QUINT coordinates do not match the WHS coordinate system. What going on?