Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI

The past, present, and future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress

Predicting Parkinson's disease trajectory using clinical and functional MRI features: a reproduction and replication study

Parkinson’s disease (PD) is a common neurodegenerative disorder with a poorly understood physiopathology and no established biomarkers for the diagnosis of early stages and for prediction of disease progression. Several neuroimaging biomarkers have been studied recently, but these are susceptible to several sources of variability. In this context, an evaluation of the robustness of such biomarkers is essential. This study is part of a larger project investigating the replicability of potential neuroimaging biomarkers of PD. Here, we attempt to reproduce (same data, same method) and replicate (different data or method) the models described in Nguyen et al., 2021 to predict individual's PD current state and progression using demographic, clinical and neuroimaging features (fALFF and ReHo extracted from resting-state fMRI). We use the Parkinson’s Progression Markers Initiative dataset (PPMI, ppmi-info.org), as in Nguyen et al.,2021 and aim to reproduce the original cohort, imaging features and machine learning models as closely as possible using the information available in the paper and the code. We also investigated methodological variations in cohort selection, feature extraction pipelines and sets of input features. The success of the reproduction was assessed using different criteria. Notably, we obtained significantly better than chance performance using the analysis pipeline closest to that in the original study (R2 > 0), which is consistent with its findings. The challenges encountered while reproducing and replicating the original work are likely explained by the complexity of neuroimaging studies, in particular in clinical settings. We provide recommendations to further facilitate the reproducibility of such studies in the future

Predicting Parkinson's disease trajectory using clinical and functional MRI features: a reproduction and replication study

Parkinson’s disease (PD) is a common neurodegenerative disorder with a poorly understood physiopathology and no established biomarkers for the diagnosis of early stages and for prediction of disease progression. Several neuroimaging biomarkers have been studied recently, but these are susceptible to several sources of variability. In this context, an evaluation of the robustness of such biomarkers is essential. This study is part of a larger project investigating the replicability of potential neuroimaging biomarkers of PD. Here, we attempt to reproduce (same data, same method) and replicate (different data or method) the models described in Nguyen et al., 2021 to predict individual's PD current state and progression using demographic, clinical and neuroimaging features (fALFF and ReHo extracted from resting-state fMRI). We use the Parkinson’s Progression Markers Initiative dataset (PPMI, ppmi-info.org), as in Nguyen et al.,2021 and aim to reproduce the original cohort, imaging features and machine learning models as closely as possible using the information available in the paper and the code. We also investigated methodological variations in cohort selection, feature extraction pipelines and sets of input features. The success of the reproduction was assessed using different criteria. Notably, we obtained significantly better than chance performance using the analysis pipeline closest to that in the original study (R2 > 0), which is consistent with its findings. The challenges encountered while reproducing and replicating the original work are likely explained by the complexity of neuroimaging studies, in particular in clinical settings. We provide recommendations to further facilitate the reproducibility of such studies in the future

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.Additional co-authors: Sofie Van Den Bossche, Xenia Kobeleva, Jon Haitz Legarreta, Samuel Guay, Selim Melvin Atay, Gael P. Varoquaux, Dorien C. Huijser, Malin S. Sandström, Peer Herholz, Samuel A. Nastase, AmanPreet Badhwar, Guillaume Dumas, Simon Schwab, Stefano Moia, Michael Dayan, Yasmine Bassil, Paula P. Brooks, Matteo Mancini, James M. Shine, David O’Connor, Xihe Xie, Davide Poggiali, Patrick Friedrich, Anibal S. Heinsfeld, Lydia Riedl, Roberto Toro, César Caballero-Gaudes, Anders Eklund, Kelly G. Garner, Christopher R. Nolan, Damion V. Demeter, Fernando A. Barrios, Junaid S. Merchant, Elizabeth A. McDevitt, Robert Oostenveld, R. Cameron Craddock, Ariel Rokem, Andrew Doyle, Satrajit S. Ghosh, Aki Nikolaidis, Olivia W. Stanley, Eneko Uruñuela, The Brainhack Communit

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

International audienceBrainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress