FastSurfer – AI-Based NeuroImage Analysis Package
To provide an efficient neuroimage analysis pipeline for the medical imaging communities by consolidating advanced DL-methods into a single user-friendly, maintainable, open source software framework.
Project Lead: Martin Reuter (German Center for Neurodegenerative Diseases)
Flexible, Modular and Extensible Pipelines for Integrative Neuro-Histology
To develop an easy-to-use and validated neuroanatomical framework for the multidimensional image viewer napari, bringing state-of-the-art image analysis plugins to neuroscience.
Project Lead: Adam Tyson (Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit, University College London)
From Library to Protocol: scikit-image as an API Reference
To create a consistent, type-annotated, discoverable, and extensible API for scikit-image and facilitate interoperability in the broader image analysis ecosystem.
Project Lead: Juan Nunez-Iglesias (Monash University / NumFOCUS)
Globalization of CGAP to Advance Genome Medicine
To inspire a diverse global community to collaborate in genome medicine, research, and education by packaging CGAP’s portal and cloud infrastructure as self-serve, orchestrated, open source software.
Project Lead: Dana Vuzman (Harvard Medical School)
Improving OpenRefine’s Reproducibility
To improve OpenRefine to empower users without programming experience to publish research datasets along with verifiable and reproducible workflows, and to automate such workflows.
Project Lead: Antonin Delpeuch (Code for Science & Society)
Improving QIIME 2 pathogen identification and developer community tools
To facilitate the detection and characterization of pathogens in microbiome data, while supporting community development and dissemination of accessible and reproducible bioinformatics applications.
Project Lead: J. Gregory Caporaso (Northern Arizona University) | Nicholas Bokulich (ETH Zurich)
Improving Standard Practice for Neuroimaging Analyses with Nilearn
To scale technical and social support for new analyses in Nilearn including the general linear model, giving access to a broad statistical framework for neuroimagers within the open source Python ecosystem.
Project Lead: Jean-Baptiste Poline (McGill University)
Integrating the Software Toolkit for Protein Structure Modeling
To build a new class of macromolecular modeling methods to study the interplay of structure, dynamics, cellular assemblies, and disease from the subatomic to nanometer scale.
Project Lead: James Fraser (University of California, San Francisco)
Integration of Protégé with Other Open Tools for Ontology Engineering
To integrate the WebProtégé ontology editor with other open source tools that together constitute an ecosystem that is used widely to develop and manage biomedical ontologies.
Project Lead: Mark Musen (Stanford University)