Category Archives: oa.neuro

Helping Others Use Your Data: Lessons From the Field of Neuroscience – YouTube

Posted on by
Reply

“So you’ve created an amazing dataset that you would love for other researchers to have access to. What’s next? Join experts from NeuroImaging Data Model (NIDM) and the Max Planck Institute for Empirical Aesthetics to learn about metadata: what it is, why it is important, and how the OSF and other tools can make it easy for you to include it with your project materials so others can find the data you’ve worked so hard to curate. The STEM Education Hub is supported by the National Science Foundation (NSF) award DRL-1937698. Any opinions, findings, conclusions, or recommendations contained within the STEM Education Hub are those of the authors and do not necessarily reflect the view of NSF.”

Introducing Open Peer Review at JNeurosci | Journal of Neuroscience

Posted on by
Reply

“In our open peer review model, we will publish the editorial decision letters, reviews (in anonymized form), and the authors’ responses to the critiques along with the article. That is, we will disclose the entire process that led to the publication of an article, including the contributions of editors, reviewers, and authors. Please note that we will honor and maintain the confidential nature of the process by keeping the anonymity of our reviewers (if they do not indicate otherwise by signing their reviews).

We understand that not everyone in our community may embrace our open peer review model from the get-go. In our version of the model, we will give both authors and reviewers the ability to opt out. Authors will be asked whether their rebuttal can be published only at the initial manuscript submission stage; reviewers can opt out of sharing their anonymous review when submitting initial comments about a paper. That way, we hope to minimize biases that may result from possible outcomes of the peer review process. Tracking the opt out choice will also be a valuable measure of how our community is reacting to the new open peer review at JNeurosci….”

Helping Others Use Your Data: Lessons From the Field of Neuroscience

Posted on by
Reply

“So you’ve created an amazing dataset that you would love for other researchers to have access to. What’s next? Join experts from NeuroImaging Data Model (NIDM) and the Max Planck Institute for Empirical Aesthetics to learn about metadata: what it is, why it is important, and how the Open Science Framework and other tools can make it easy for you to include it with your project materials so others can find the data you’ve worked so hard to curate.

 

Data sharing in neuroimaging: experiences from the BIDS project | Nature Reviews Neuroscience

Posted on by
Reply

Abstract:  Data sharing is an essential component of open science practice. The Brain Imaging Data Structure project has pioneered a way to organize neuroimaging and behavioural data that enables easy sharing and reuse. We present experiences from the BIDS project and highlight how standards can promote open science.

 

Scientists generate first single-cell atlas of the primate brain

Posted on by
Reply

“A longstanding mystery in science is how the over 100 million individual neurons work together to form a network that forms the basis of who we are—every human thought, emotion and behavior….

“Our data, which we have made open and available to the scientific community and broader public, represent the largest and most comprehensive multimodal molecular atlas in a primate to date, and are crucial for exploring how the many cells of the brain come together to give rise to the behavioral complexity of primates including humans,” said senior co-author Jay Shendure, a professor of Genome Sciences at the University of Washington and Director of the Brotman Baty Institute….

Together, “multi-omic” atlas now provides an open resource to the worldwide research community for further investigations into the evolution of the human brain and identifying novel targets for disease interventions.”

Letter from the Editor-in-Chief: Neurotherapeutics’ Transition to Gold Open Access | SpringerLink

Posted on by
Reply

“Beginning with the January 2024 issue, Neurotherapeutics will become a fully Open Access journal in keeping with the overall trend in scientific publishing. Over the years, the official journal of the American Society for Experimental Neurotherapeutics (ASENT) has gone through a number of transitions regarding its publishing model, beginning with traditional subscription-based print journal paid by libraries, universities, and other institutions, then hybrid online publishing with both subscription and open access options, and now moving to fully open access where the cost of publishing will be covered by authors, their funders, or institutions. Invited articles will not be subject to Article Processing Charges. Along with this change, Elsevier will now be the new publisher of Neurotherapeutics.”

A Large Open Access Dataset of Brain Metastasis 3D Segmentations with Clinical and Imaging Feature Information – PMC

Posted on by
Reply

Abstract:  Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

 

OS Workshop 2023 – Bordeaux Neurocampus | Welcome to the first edition of the Bordeaux Neurocampus Open Science Workshop, to be held in October 2023.

Posted on by
Reply

“Welcome to the first edition of the Bordeaux Neurocampus Open Science Workshop, a 5-day workshop dedicated to promoting Open Science principles.

This edition will take place from October 16th to October 20th, 2023.”

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community | PLOS Computational Biology

Posted on by
Reply

Abstract:  The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.

 

Sharing neurophysiology data from the Allen Brain Observatory | eLife

Posted on by
Reply

Abstract:  Nullius in verba (‘trust no one’), chosen as the motto of the Royal Society in 1660, implies that independently verifiable observations—rather than authoritative claims—are a defining feature of empirical science. As the complexity of modern scientific instrumentation has made exact replications prohibitive, sharing data is now essential for ensuring the trustworthiness of one’s findings. While embraced in spirit by many, in practice open data sharing remains the exception in contemporary systems neuroscience. Here, we take stock of the Allen Brain Observatory, an effort to share data and metadata associated with surveys of neuronal activity in the visual system of laboratory mice. Data from these surveys have been used to produce new discoveries, to validate computational algorithms, and as a benchmark for comparison with other data, resulting in over 100 publications and preprints to date. We distill some of the lessons learned about open surveys and data reuse, including remaining barriers to data sharing and what might be done to address these.

 

World’s first completely open- and crowd-sourced neuroscience experiment launched

Posted on by
Reply

“Today, scientists from the Allen Institute for Neural Dynamics, a division of the Allen Institute, launched the world’s first completely open- and crowd-sourced neuroscience experiment-;inviting researchers from around the world to publicly design a shared experiment that will run on the Allen Brain Observatory, as part of the Institute’s OpenScope program. Experiments will probe the dynamic functions of the brain and how cells interact and communicate to produce thoughts and actions and shed light on how we make complex decisions….

Any scientist is now able to join the public forum (https://community.brain-map.org) and suggest research questions and experimental methods to be discussed amongst the community. The community will then vote to select one OpenScope project to be conducted by the Allen Institute. Every phase of design, implementation, and data output will be completely open….

Launched five years ago, OpenScope was inspired by shared astronomical observatories like the Hubble Space Telescope where outside researchers can conduct cutting edge experiments too expensive for individual labs using NASA’s powerful tools and technology. Likewise, OpenScope aims to bring the large-scale standardization of the Allen Institute’s neuroscience platforms to scientists around the world….”

Open-Access Journals can pave access to Global Neurosurgery – ScienceDirect

Posted on by
Reply

“Joint ventures between the HIC and LMIC scientists for research in the LMIC native country with adequate funding for research and publication can be launched to promote more participation of LMIC researchers in publications. Policies by the HIC neurosurgical bodies and publishing authorities to let LMIC authors share knowledge more by extending the waiver options for the authors can make the globalization of neurosurgery meaningful. Training of LMIC neurosurgeons, which can be conducted virtually also, on research methodology, and manuscript preparation along with international research mentorship can easily be carried out, so that they can participate in publishing their research works more efficiently.

The limited knowledge sharing from the LMIC is depriving the global scientific community of the diverse treasure trove of neurosurgical cases in these regions. Recognizing how these countries manage the huge number of patients with very limited resources can truly prove valuable in improving global neurosurgical services altogether. PMOA journals can play a pivotal role in that….”

Team Neurodiversity: Integrating neurodiversity and open scholarship

Posted on by
Reply

“This team is responsible for discussing how open scholarship can be used to support the neurodiversity movement and enhance connections between open scholarship and neurodiversity; and how neurodiversity and open scholarship can intersect to make higher education more inclusive and accessible….”