Workflow Description

The QUINT workflow facilitates the quantification and spatial analysis of labelled features in images of histological sections from the rodent brain using 3D reference atlases. The workflow is built on the following open access software:

• ilastik allows the extraction of labelled features such as cells, using machine learning image segmentation.
• QuickNII generates custom-angle slices from volumetric brain atlases to match the proportions and cutting plane of histological sections.
• VisuAlign is then used for nonlinear alignment of the reference atlas slice to the section image..
• 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.