5. Quantification and spatial analysis with Nutil

Version 10.1 by sharoncy on 2020/03/28 15:37

Nutil Quantifier

A detailed user manual is included when downloading the software.

Quantifier.PNG

Basic steps:

Nutil Quantifier quantifies and assigns anatomical location to labelled objects 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 GUI (e.g. 255, 0, 0 for red).

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 atlas maps

Generate the atlas maps in FLAT format with the QuickNII software (or with VisuAlign).

  1. Anchored XML file generated with the QuickNII software.

Illustration seg_flat_files.png

Reference atlases available in Nutil Quantifier

The Nutil software is currently compatible with the Allen mouse brain Atlas v3 (2015 or 2017) and the Waxholm Space Atlas of the Sprague Dawley Rat v2 or v3.