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Analyse neuroscience data in a 3D brain atlas space

By spatially registering images to a 3D atlas, analyses can be performed based on regions of interest specified by the atlas maps.

Atlas-driven analysis tools

All tools and software


JuGEx is a tool that combines data from two repositories, the Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, to provide detailed insights into how gene activities and microanatomical architectures contribute to brain function and dysfunction. The Allen Human Brain Atlas contains regional gene expression data, while the EBRAINS human brain atlas offers three-dimensional cytoarchitectonic maps reflecting interindividual variability. JuGEx integrates tissue transcriptome and probabilistic brain segregation data, allowing researchers to explore the complex relationships between genetic expression, brain structure, and function. With JuGEx, researchers can gain a deeper understanding of the intricate connections between genes and cognition, which can inform the development of new treatments for brain disorders and improve our understanding of brain function in health and disease.

Brain atlases


Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.

Data analysis and visualisationBrain atlases


Nutil aims to simplify the pre-and-post processing of 2D brain section image data from mouse, rat and other small animal models. It can be used to preprocess images in preparation for analysis, and used as part of the QUINT workflow to perform spatial analysis of labelled features relative to a reference brain atlas. Nutil is developed as a stand-alone application with a simple user-interface, requiring little-to-no experience to execute.

Brain atlasesData analysis and visualisation

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