If you have any further question concerning open science practices in general, BIDS and the tools we are developing around this data structure or our study group don’t hesitate to contact me via:
The device center ‘Tools for Open and Reproducible Neuroscience’ aims at offering tools/software solutions to support researchers to work more transparently and reproducibly.
The main focus here lies on implementing software for the two main devices centered in the neuroimaging unit:
- Elekta/MEGIN Neuromag MEG system
- Siemens Prisma 3T MRI system
One of the key aspects for transparent and reproducible research is an overarching and unifying data structure which has rich metadata describing different aspects of the acquisition and experiment. The most established data structure aiming at fulfilling the role of an overarching structural organization of neuroimaging datasets is the Brain Imaging Data Structure (BIDS). BIDS is a community driven and open source effort which is constantly evolving to best fit the needs of a broad range of researchers originating from different fields within the neuroimaging domain.
Using such data structure facilitates collaborative research since there is no need to explain the data due to its commonly known structural organization. Moreover it eases the sharing of data and allows for meta analyses and big data approaches, which are referred to as gold-standard scientific practices. Since data organization is such an important and fundamental topic within the open science community our projects are centered around BIDS.
- ancpBIDS: ancpBIDS is a lightweight python library to read/query/validate/write BIDS datasets.It provides a unified and modality agnostic I/O interface for researchers to handle BIDS datasets in their workflows or analysis pipelines. Its implementation is based on the BIDS schema and allows to evolve with the BIDS specification in a generic way.
For more detailed information about that library and for those who want to contribute to this open-source project check out the GitHub: ancpBIDS.
- BIDS Conversion GUI: We are currently developing an app with the purpose of converting all the data acquired at the devices in our unit (see above) into the BIDS standart. The app is implemented as a user-friendly GUI performing the conversion with minimal user input. Moreover we are currently working on the integration of new data into already existing project directories such that projects which have stopped for some reason, e.g. researchers leaving the university, can easily be continued by other researchers.
- MEGqc: Neuroimaging data is prone to many sources of noise or artifacts. That being said it seems logical that one should assess the quality of the data before analyzing them to not run into problems during the analysis because of poor data quality. Mriqc is a tool to automatically assess the quality of MRI data. The MEG community however lacks such software. For this reason we are currently developing a quality control tool in the domain of MEG. As is the case for mriqc, this tool will be based on BIDS and perform automated quality assessment given a BIDS conform MEG data set.
- We organized a BIDS user schooling, encouraging students/staff to use BIDS for storing and managing their data and providing them with general information about BIDS and how to use the tools we are developing around this data structure.
- We organized an international workshop ‘open and reproducible neuroimaging - integration of community developed tools from data acquisition to publication’.
- This workshop yielded a collaborative paper about open science practices from study inception to the publication of results or data. The preprint can be found here. Note, that this paper is accompanied by a nicely structured table containing over 250 resources, including tools to use for the different steps of open scientific work, websites with tempaltes for consent forms and many more. This table can be found here.
- We are accepted by the INCF to mentor contributors of the Google Summer of Code 2022 (GSoC) in two sub projects within the ancpBIDS project
- We plan to organize annual international workshops/conferences centered around open science related topics to keep in touch with the community. We will therefore invite renowned speakers to present and discuss current developments within the community.
- Continue with BIDS user schoolings at least twice a year to ensure acceptance and usage of this data format within our department.
If you want to participate or be kept up-to-date about our study group feel free to join our biweekly BBB meetings here. The meetings take place every even calendar week on Tuesdays between 12:00-13:00. Moreover, if you are associated with the University of Oldenburg (student or staff) you can send a membership request to join our study group in StudIP here.
In our meetings we present and discuss the progress of our projects or give introductory talks on open science related topics like BIDS or useful tools for reproducible and transparent research.