Nutil

Nutil performs preprocessing, format conversion, transformation, and atlas-based quantification of large tiled histological images to support analysis of rodent (mouse and rat) brain sections using QuickNII-derived 3D atlas maps.

Key Features:

• Efficient Software Design: Implemented in C++ for high-performance processing of large image datasets.
• Transform: Performs image manipulations including rotation, mirroring, scaling, resizing, and renaming of large tiled TIFF images common in histology.
• TiffCreator: Generates tiled TIFF images from PNG and JPEG input formats.
• Resize: Downscales PNG and JPEG images and outputs PNG files for downstream analysis.
• Quantifier: Quantifies segmented objects within brain sections using regions defined by brain atlas maps generated with QuickNII based on 3D reference atlases (mouse or rat), and produces report files, point cloud coordinate files for visualization in reference atlas space, and superimposed color-coded atlas images highlighting specific objects.
• Multi-core Processing: Leverages multi-core processing capabilities to handle large datasets efficiently.

Scientific Applications:

• Brain connectivity mapping: Enables quantification and spatial mapping of labeled structures across whole rodent brain sections for connectivity studies.
• Cellular and structural analysis: Supports analysis of cellular structures and object quantification within anatomical reference space.
• Molecular and pathological investigations: Facilitates comparison of molecular organization and histological changes across normal and pathological rodent brain tissue.

Methodology:

Performs image transformations (rotation, mirroring, scaling, resizing, renaming, and tiled TIFF creation), quantification of segmented objects referenced to QuickNII-generated 3D atlas maps, and leverages multi-core processing for large datasets.