1. Introduction

Quantifier is an integral part of the QUINT workflow. It support quantification of labelled features in image series of histological sections from mouse and rat brain based on a reference atlas. The following atlases are currently supported:

  • Allen Mouse Brain Atlas Common Coordinate Framework version 3 (2015 and 2017) (integrated in Nutil)

  • Waxholm Atlas of the Spraque Dawley Rat, version 2, 3 and 4 (integrated in Nutil)

  • Kim Unified Mouse Brain Atlas version 1 (2019) (integrated in Nutil v1.0.0)

  • Custom atlases such as the Developmental Mouse Brain Atlas (DeMBA P4-P56) (use the custom atlas option)

Warning

QUINT does not support quantification for regions that fall outside of the reference atlases, or quantification without use of an atlas.

Watch our video utorial:

Quantifier requires three sets of input:

  1. Atlas maps in FLAT format (generate with QuickNII or VisuAlign).

  2. Registration information in JSON format (from QuickNII, VisuAlign or DeepSlice).

  3. Images with the features to be quantified displayed with a unique RGB colour code (indexed 8-bit PNG format) (generated with ilastik or another image analysis tool).

It generates three sets of results:

  1. Reports with counts and percentage coverage per reference atlas region. There is also the option to generate reports for customized regions (compilations of reference atlas regions) (CSV format).

  2. Images with the segmentations superimposed on the atlas maps (PNG format).

  3. Point clouds for visualising the extracted features in the MeshView Atlas Viewer (JSON format).

As the QUINT workflow requires the use of several software, this section is split into several parts with information on how to prepare the input files, how to run Quantifier, and how to interpret the results.