Description

The QUINT workflow enables an atlas based analysis of extracted features from histological image sections from the rodent brain using 3D reference atlases. 

Examples of use are: cell counting and spatial distributions; determination of projection areas in connectivity experiments; exploration of pathological hallmarks in brain disease models. Integration of various data to the same reference space enables new exploration strategies and re-use of experimental data.

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.

QUINT workflow video

Workflow highlights

• The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.