Nutil: Neuroscience Image Processing and Analysis Utilities

Nutil documentation

• Introduction
• Installation and citation
  • Technical information
  • System Requirements
  • Conditions of use
  • Citation of Nutil
  • Citation of the reference atlases
• Release notes
  • Nutil v1.1 (Quantifier only)
  • 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 JSON file
• 3. How to run Quantifier
  • 3.1. Python plots
• 4. Object splitting explained
• 5. Custom masks explained
  • 5.1. QuickMask
• 6. Custom regions explained
  • 6.1. Custom Region reports
  • 6.2. Coordinate output
• 7. How to interpret the results
  • 7.1. RefAtlasRegion reports
  • 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. Transform: “Maximum TIFF file size exceeded”, what do I do?
  • 9.4. Quantifier: There are no object counts in the reports (N/A)?
  • 9.5. Quantifier: The CSV reports don’t open correctly in Microsoft Excel
  • 9.6. Quantifier: I don’t understand what to enter for the Pixel Scale?
  • 9.7. Quantifier: How do I calculate the Pixel Scale of images that have been downscaled?
  • 9.8. Quantifier: The QUINT coordinates do not match Allen Common Coordinate Framework coordinates. What’s going on?
  • 9.9. Quantifier: The QUINT coordinates do not match the WHS coordinate system. What going on?
  • 9.10. Quantifier: How do the QUINT coordinates for mouse (Allen CCFv3) relate to Bregma?
  • 9.11. Quantifier: How do I assign reference atlas regions to the coordinates extracted by Nutil?
  • 9.12. Quantifier: Is it possible to extract coordinates corresponding to the the centroid of my features-of-interest?
  • 9.13. Quantifier: Can I use my own atlas in Nutil?