Nutil Quantifier

A detailed online user manual is found here.

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 a single RGB colour

Requirement

• Input format: 24-bit RGB images in PNG.
• The images have to have the same aspect ratio 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.

2. Customised atlas maps

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

3. Anchored XML file generated with the QuickNII software.

Reference atlases in Nutil Quantifier

The Nutil software is currently compatible with

• Allen mouse brain Atlas (CCFv3, 2015 or 2017) and
• Waxholm Space Atlas of the Sprague Dawley rat brain v2, v3, v4.