The EBRAINS Collaboratory offers researchers and developers a secure environment to work with others. You control the level of collaboration by sharing your projects with specific users, teams or all of the Internet. Many researchers are sharing their work already; several services, tools, datasets, and other resources are publicly available, and many more are available for registered users.
The JuGEx tool combines the analytical benefits of The Allen Human Brain Atlas and the EBRAINS Human Brain Atlas for integrating tissue transcriptome and probabilistic brain segregation.
- Combine the analytical benefits of the comprehensive maps of the EBRAINS human brain atlas with the transcriptomics data offered by the Allen Brain AtlasObtain quantitative measures of labelled structures in atlas-defined regions
- Perform your analysis in Python, Matlab, or using an intuitive graphical plugin of the EBRAINS Interactive Atlas Viewer
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.
Differential gene expression analysis using EBRAINS human brain atlas
The principle of JuGEx is simple: Select two brain areas from the EBRAINS human brain atlas and a set of candidate genes of your interest. JuGEx will use probabilistic maps of brain regions to extract gene expression measurements from the Allen Brain Atlas (© 2015 Allen Institute for Brain Science), and perform a differential analysis of the genes and associated factors in the two brain regions. As a result, you obtain the computed p-values together with the extracted transcriptomics data, and can visually inspect the locations of the data samples in atlas reference space.
JuGEx is available to you in different forms: As a Matlab implementation, as a Python implementation included in the siibra Python client, and as an interactive Plugin included in the EBRAINS Atlas Viewer, accessible from your browser right away. Choose the implementation that suits you the best.
Bludau S., Mühleisen T. W., Eickhoff, A. B., Hawrylycz M. J., Cichon S., Amunts K. (2018) Integration of transcriptomic and cytoarchitectonic data implicates a role for MAOA and TAC1 in the limbic-cortical network. Brain Structure and Function. https://doi.org/10.1007/s00429-018-1620-6
Other softwareAll software
The EBRAINS multilevel human brain atlas provides detailed information on anatomy, connectivity, and function. It links macroanatomical concepts and their intersubject variability with measurements of the microstructural composition and intrinsic variance of brain regions.
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.