5. Quantification and spatial analysis with Nutil

Version 2.5 by puchades on 2020/03/25 15:33

Nutil Quantifier

A detailed Nutil user manual is included when downloading the software.

Basic steps:

Quantifier locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:

  1. Segmentations with the labelling displayed in one RGB colour

Requirement:

  • must be 24-bit RGB images in PNG format
  • same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
  • Quantifier is only able to extract one RGB colour at a time. Apply one RBG colour to all of the objects of interest, and specify this colour code in the Excel template.

To generate the segmentations we recommend the Pixel and Object Classification workflows in the ilastik software (ilastik.org). However, any image analysis software may be used.

  1. Customised anatomical atlas maps

Generate the atlas maps in FLAT format with the QuickNII software

  1. Anchored XML file generated with the QuickNII software.
  2. Reference atlas label file (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the Nutil package (in the “Labels” folder).