Nutil: Neuroscience Image Processing and Analysis Utilities
- 1. Introduction
- 2. Preparing the input files
- 3. How to run Quantifier
- 4. Object splitting explained
- 5. Custom masks explained
- 6. Customised reports explained
- 7. How to interpret the results
- 8. Warnings and error messages
- 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 reports (CSV) 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?