Workflow Description

The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software:

1. ilastik allows the extraction of labelled features such as cells by segmentation.
2. QuickNII generates atlas maps customised to match the proportions and cutting plane of the brain sections. VisuAlign enables nonlinear adjustments of the reference atlas to the experimental section.
3. Nutil enables image transformations, in addition to quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII.

In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.

Workflow highlights

• The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge.