Open sina-mansour opened 10 months ago
Fig. 1 Cerebro – A Python-Based 3D Brain Visualization Tool. (a) Cerebro leverages an extensive array of open-source Python tools, forming a robust foundation for its functionality. It also integrates with these tools to enable seamless Pythonic neuroimaging visualizations. (b) Cerebro prioritizes principles of scriptability, reproducibility, visualization quality, cross-compatibility, and integration in its pursuit of providing a reliable solution for the neuroimaging community. (c) An illustrative Cerebro-generated visualization, accompanied by a scannable QR code linked to the publicly accessible reproduction scripts.
Ping: @anniegbryant @clarkenj @Niousha-Dehestani @jaysonjeg @tkkuehn @kaitj @dsleiter
This is our submission for the OHBM Brainhack 2023 proceedings.
Awesome! I no longer have access to that email unfortunately, if it's not too late my email is natashajayne@gmail.com. But no worries :)
hello all, could you please provide the authors information in the following link by May 15th? https://docs.google.com/forms/d/e/1FAIpQLSckbC4F6KOtge1KOyzwj5yIbWR7tB8HrnqQ4KPZB7Mr3UcvMw/viewform
Authors
Sina Mansour L. sina.mansour.lakouraj@gmail.com Annie G. Bryant abry4213@uni.sydney.edu.au Natasha Clarke natashajayne@gmail.com Niousha Dehestani ndehestanikolag@deakin.edu.au Jayson Jeganathan jayson.jeganathan@gmail.com Tristan Kuehn tkuehn@uwo.ca Jason Kai tkai@uwo.ca Darin Erat Sleiter darin@ae.studio Maria Di Biase <maria.dibiase@unimelb.edu.au > Caio Seguin caioseguin@gmail.com B.T. Thomas Yeo thomas.yeo@nus.edu.sg Andrew Zalesky azalesky@unimelb.edu.au
Summary
Synopsis
Openness and transparency have emerged as indispensable virtues that pave the way for high-quality, reproducible research, fostering a culture of trust and collaboration within the scientific community $^1$. In the domain of neuroimaging research, these principles have led to the creation of guidelines and best practices, establishing a platform that champions openness and reproducibility $^2$. The field has made substantial strides in embracing open science, a feat achieved through the successful integration of open-source software $^3$, public dataset sharing $^4$, standardized analysis pipelines $^5$, unified brain imaging data structures $^6$, open code sharing $^7$, and the endorsement of open publishing.
The joint efforts of these initiatives have established a robust foundation for cultivating a culture of collaboration and accountability within the neuroimaging community. Nonetheless, amidst these advancements, a crucial inquiry arises: What about the visual representations —the very tools through which we observe and make sense of neuroimaging results? It is within this context that we introduce "Cerebro" $^8$, a new Python-based software designed to create publication-quality brain visualizations (see Fig.1). Cerebro represents the next step in the quest for openness and reproducibility, where authors can share not only their code and data but also their publication figures alongside the precise scripts used to generate them. In doing so, Cerebro empowers researchers to make their visualizations fully reproducible, bridging the crucial gap between data, analysis, and representation.
Future guidelines
As Cerebro continues to evolve in its early development stages, this manuscript serves as a manifesto, articulating our dedication to advancing the cause of open and reproducible neuroimaging visualization. Cerebro is guided by a set of overarching goals, which include:
Fully Scriptable Publication-Quality Neuroimaging Visualization:
Cerebro's primary mission is to equip researchers with the means to craft impeccable brain visualizations while preserving full scriptability. Cerebro enables researchers to document and share every aspect of the visualization process, ensuring the seamless reproducibility of neuroimaging figures.
Cross-Compatibility with Different Data Formats:
The diversity of brain imaging data formats can pose a significant challenge for visualization. Many existing tools are constrained by compatibility limitations with specific formats. Drawing upon the foundations laid by tools like NiBabel $^9$, Cerebro is determined to provide robust cross-compatibility across a wide spectrum of data formats.
Integration with Open Science Neuroimaging Tools:
We wholeheartedly acknowledge that Cerebro cannot thrive in isolation. To realize its full potential, it must seamlessly integrate into the existing tapestry of open science tools, software, and standards. Through active collaboration with the neuroimaging community, particularly through open, inclusive community initiatives such as brainhacks $^{10}$, Cerebro aspires to forge cross-compatibility with established and emerging tools, standards, and pipelines. Our vision is one where the future of neuroimaging visualizations is marked by unwavering openness and reproducibility, fostered by this united effort.
References (Bibtex)
References
Bibtex bibliography