Open Science Grants is a grant program from the Chan Zuckerberg Initiative (CZI) that funds tools, platforms, and organizations advancing the open and immediate sharing of scientific knowledge, processes, and outputs. CZI invests in infrastructure that makes the scientific process more open, reproducible, and collaborative, enabling scientists globally to build on each other's work.

The program supports education and capacity building, open-source biomedical software, and reproducibility tools spanning areas such as single-cell genomics, bioimaging, and computational biology. Eligible applicants include academic institutions, nonprofits, and open-source scientific software projects demonstrating community impact.

CZI maintains a publicly browsable directory of current and past grantees representing multiple funding cycles across its Essential Open Source Software (EOSS) and related programs.

Open Science Grants - Chan Zuckerberg Initiative CZI’s Open Science program aims to advance the universal and immediate open sharing of all scientific knowledge, processes, and outputs. To this aim, we invest in tools, platforms, and organizations that help expand participation and access to the scientific process by making it open and reproducible, and helping scientists build on each others’ work. Browse all our grantees below.

Education & Capacity Building International Interactive Computing Collaboration (2i2c) 2i2c makes interactive computing more accessible and useful for research and education by managing interactive computing infrastructure.

3D Slicer for African Scientists: Enabling AI for Health To empower African scientists to develop 3D Slicer AI-based extensions for health priorities and enable their deployment to global communities through customized AI models for multilingual translation. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

3D Slicer for Latin America: Localization and Outreach To empower the biomedical research community in Latin America by localizing 3D Slicer to Spanish and Portuguese, improving tutorial localization infrastructure, and holding outreach events.

3D Slicer in My Language: Internationalization and Usability Improvements To increase the accessibility of the 3D Slicer open source platform for biomedical research to clinicians and scientists in non-English speaking countries. A Hub for Probabilistic Analysis for Single-Cell Genomics To develop scvi-tools 2.

0: an accessible and scalable environment for probabilistic modeling for single-cell genomics that enables the next generation of massive-scale studies.

A Modular Suite of Advanced Bioimaging Tools with scikit-image and Dash To bring the combined power of scikit-image and Dash to a larger number of scientists thanks to increased execution speed, interactive image annotation and processing, and outstanding documentation targeting life sciences practitioners.

A Solid Foundation for Statistics in Python with SciPy The project will improve the SciPy library's statistics functionality to better serve biomedical research and downstream projects. In addition, an outreach component will engage female students, inspiring them to participate in open source code development.

A Unified Framework for Cell-Cell Communication Modeling To develop an open source, unified framework for cell-cell communication modeling and exploration that is available to the entire scientific community.

Accessible Interactive Data Visualizations in Python with Bokeh To address accessibility gaps in Bokeh, Panel, and Holoviz by incorporating accessibility affordances to ensure everyone can benefit from their powerful data visualization capabilities. Achieving Accessibility for UpSet Plots To make UpSet plots accessible to low-vision and blind users, and to simplify authoring UpSet plots.

Adapting limma and edgeR for Single-cell and Proteomics To address new challenges posed by replicated single-cell RNA-seq data and by mass spectrometry proteomics.

Advancing an Inclusive Culture in the Scientific Python Ecosystem To support the onboarding, inclusion, and retention of people from historically marginalized groups on scientific Python projects and structurally improve the community dynamics of NumPy, SciPy, Matplotlib, and pandas.

Advancing Array Interoperability Within the PyData Ecosystem To advance array interoperability within the PyData Ecosystem by accelerating Array API adoption in key libraries used in biomedical research and building infrastructure for measuring API compliance.

Advancing Microbiome Research Through QIIME 2 Community Development To support the QIIME 2 user and developer communities by enabling sharing of automatically tested third-party content on the QIIME 2 Library, and hosting our first-ever co-convened user and developer workshop and networking event.

To enhance the anndataR package for improved interoperability and functionality in handling single-cell data within the R programming environment.

Apache Arrow Apprenticeship Program for OSS Maintenance and Community To support the growth, sustainability, and diversity of the Apache Arrow project by expanding an apprenticeship program, which recruits developers from underrepresented groups and trains them to be open source software maintainers.

Promoting preprints and open, rapid dissemination in the life sciences Automated Generation of Galaxy Tools To develop software that is able to automatically integrate existing open source software into the Galaxy platform. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Automated Optimal Model Calibration for the OpenSim Biomechanics Simulator To develop an automated tool that uses optimization to calibrate models of the musculoskeletal system and improve simulation results, and disseminate the tool to the OpenSim community with documentation, examples, case studies, and outreach events.

Bacterial Variant Calling with Snippy To develop a modular and extensible variant caller for microbial genome data that is sequencing technology agnostic and underpinned by an extensive validation and test suite. Bayesian Open Source Software for Biomedicine: Stan, ArviZ and PyMC3 To develop key infrastructure updates and collaboration resources for state-of-the-art Bayesian modeling software libraries.

bcbio-nextgen: Reproducible, Community Developed Analysis Pipelines To provide ongoing maintenance and community support for the bcbio-nextgen toolkit, focusing on existing variant calling functionality and improving the epigenomic pipelines.

Bioconductor Build System: Continuous Integration and Developer Feedback To reengineer the Bioconductor build system for nightly continuous integration, production, and distribution of tarballs and binaries for over 1,700 user-contributed software packages.

Bioconductor: High Quality Training and Support for a Worldwide Community To provide Bioconductor training globally by redeveloping the website and developing infrastructure to deliver high quality community-led training in local languages.

Bioconductor: Sustaining a Worldwide Community of Genome Data Scientists To increase participation of underrepresented groups in genome data science research through alliances with organizations advancing diversity in science, increased mentoring activities for developers, and enhanced governance of Bioconductor. Preprint servers allow scientists to rapidly share results and manuscripts before they are peer reviewed.

The Black in AI Academic Program is a resource supporting Black junior researchers as they apply to graduate programs, navigate graduate school, and enter the postgraduate job market. Bokeh Raster Image and Time Series Improvements for Biomedical Applications To extend the open source Bokeh library to cover streaming gridded visualizations for bioscience applications that currently require expensive proprietary tools.

Bridging the Gap In Medical Image Analysis and Biomechanics with ITK-SNAP This grant supports implementation of biomechanical analysis features in ITK-SNAP, an open source application for medical image segmentation, with the goal of streamlining image processing, anatomical modeling, and tissue mechanics analysis from clinical image data. Bringing GPU Scientific Visualization to the Web with VisPy 2.

0 To bridge the gap between the desktop and the web for large-scale GPU scientific visualization by developing a web version of VisPy 2. 0 based on Python, WebAssembly, WebGPU, and Datoviz. Bringing Micro-Manager to Classrooms and the Cutting-Edge To create a versatile, inclusive, open source microscopy platform for diverse global educational and research communities by modernizing and extending Micro-Manager.

Building Pediatric and Clinical Data Pipelines for MNE-Python To enhance MNE-Python for clinical neuroscience uses by improving spectral and spectro-temporal data handling, and by providing standardized preprocessing pipelines for data.

Capacity building in bioinformatics for and from Latin America To leverage regional research interests and expertise to build computational capacity across Latin America, supporting a variety of activities from workshops to knowledge exchange meetings.

Code Contribution for Women in Network Science To develop tools, training materials, and mentorship opportunities to help women and nonbinary people in network science to use and contribute code to the igraph open source network analysis library.

cogent3 Python APIs for IQ-TREE and GraphBin via a Plug-In Architecture To enhance metagenomic analysis by integrating cogent3, GraphBin and IQ-TREE to support innovative genomic technologies for monitoring the impact of viral and bacterial diversity on human health. ReviewR: a new review, assessment, and discussion platform for preprints, powered by Hypothes.

is To build an open source solution to power commenting, review, assessment, and discussion initiatives and provide a platform for the evolution of peer review. Comprehensive, Scalable, and Collaborative Single-Cell Analysis with Seurat To develop extensive functionality, expand user support, and initiate new modes of community outreach for Seurat, an open-source R toolkit for integrative single-cell analysis.

Comprehensive, Scalable, and Collaborative Single-Cell Analysis with Seurat To develop extensive functionality, expand user support, and facilitate interoperability for Seurat, an open source R toolkit for integrative single-cell analysis.

Computational Biology Software Maintenance Framework To reorganize the libSBML and Deviser code bases for better community involvement, spin out part of libSBML as a reusable component for Deviser and other projects, and establish protocols for long-term sustainability of these important resources.

Computational Tools for Population-Scale Single Cell Genomics To develop statistically robust, computationally efficient, and maximally compatible open source software for the design and analyses of multiplexed single-cell sequencing experiments.

Connecting Open Source Biomolecular Software Communities To effectively support community building efforts across open source ecosystems in molecular sciences, improve contributor pipelines, and seek synergies and collaboration opportunities in this space. Continuous Improvement to Essential High-Throughput Bio-Sequence Aligners To maintain BWA and improve the performance and robustness of BWA and its next major version BWA-MEM2.

Cytoscape Explore for Biological Networks Brings Cytoscape to the Cloud To build Cytoscape Explore, a web-based biological network viewer and editor that will make key aspects of the widely used Cytoscape application accessible to new audiences as part of its evolution from a desktop application to a cloud ecosystem.

A global community for people underrepresented in data science Accelerating global adoption and technical integration identifiers for research outputs To create value for DataCite members through community-driven, innovative, open, integrated, usable, and sustainable services for research.

This grant will enable DataCite to make great strides in their systems, processes, and advocacy work supporting researchers’ ability to get credit and recognition for their open research output, as well as further their efforts to build out their international capacity and engagement program that provides regional support and engagement in lesser represented regions such as Latin-America, Africa, the Middle East and Asia.

Deep Probabilistic Programming for Biology with Pyro To accelerate single-cell biology methods research and empower their developers with foundational probabilistic AI software. DeepGaitLab: Reconciling Vision-Based Motion Tracking with ISB Standards To interface recently developed computer vision tools with an open-source biomechanical modeling software, which should facilitate the uptake of markerless motion tracking in biomedicine.

DeepLabCut AI Residents for Next-Gen Animal Behavior To develop a DeepLabCut AI Residency Program for underrepresented groups in machine learning and computer science in order to recruit, fund, and nurture the next generation of open source leaders. DeepLabCut: A Software Package for Animal Pose Estimation To provide maintenance, user-focused extensions, education, and support of the growing DeepLabCut software community.

DeepLabCut: An Open Source Toolbox for Robust Animal Pose Estimation To support the maintenance, new extensions, and education of users of the DeepLabCut software community. DeepLabCut: An Open Source Toolbox for Robust Animal Pose Estimation To support code maintenance, a new code cookbook, and user education for the DeepLabCut software community and set the foundation towards becoming a sustainable software package for years to come.

Delivering High-Quality Bioconductor Training for a Worldwide Community To expand the global Bioconductor-Carpentries training program, increase equity and accessibility using culturally sensitive AI translation, and build capacity for workshops in Africa Democratizing Deep Learning for Microscopists with DL4MicEverywhere To establish DL4MicEverywhere, a containerized deep learning for microscopy toolkit extending the easy-to-use ZeroCostDL4Mic, with interactive notebooks for training and deployment across platforms.

Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6. Expanding usage of the DocMaps framework To make preprint review and other editorial processes machine-readable and discoverable. dynverse: A Toolkit for Studying Cell Development with Single-Cell Omics Single-cell biology is the application of technologies that enable multi-omics investigation at the level of a single cell.

This project will streamline trajectory inference from single-cell omics data by improving integration with upstream and downstream analysis pipelines.

Enabling Biomedical Science with Common Workflow Language To enable portability of complex biomedical workflows across different clouds and on-premise environments via better documentation, community support, and tooling for Common Workflow Language (CWL) with examples using Arvados and from the Personal Genome Project.

Enabling Differential Analyses of Genomic Data with limma, edgeR and Glimma To improve ease of use and interoperability of these packages, make methodological responses to new data challenges, refresh the documentation and structure of these packages, and prepare training materials.

Engaging Native American Students in Scientific Computing with QIIME 2 To use QIIME 2 as an on-ramp to scientific computing for Native American students by engaging locally with schools primarily serving Native Americans, while expanding the global QIIME2 user, developer, and educator communities.

Enhancing Diversity in Computational Mass Spectrometry To increase diversity in computational mass spectrometry through teaching and mentoring with the open-source framework OpenMS. Enhancing Giotto for Spatial Multi-Resolution Technologies To enhance Giotto by implementing a novel data structure and framework for the abstract representation and analysis of emerging datasets from multi-modal and multi-resolution spatial technologies.

Enhancing High-Level Scientific Computing Support in CuPy To provide a series of GPU accelerated routines for signal processing and interpolation in CuPy to be a foundation for the research community.

Enhancing Interoperability, UI, and Documentation of MOOSE To enhance the Multiscale Object-Oriented Simulation Environment software package through development of new GUIs, data and model import tools, and tutorials for computational modeling in neuroscience and systems biology. Note: This proposal was funded by The Kavli Foundation as part of our co-funded EOSS Cycle 6.

Enhancing Spyder IDE Remote Support for Scientific Research in Python To improve Spyder support for connecting to a remote machine to develop, execute, and debug Python code, as well as installing packages, managing environments and interacting with the remote filesystem.

Enhancing the Bactopia Ecosystem with Trainings and Visual Reports To ensure ongoing maintenance and community growth of Bactopia, focusing on integrating visual reports and comprehensive training materials.

Enhancing the Open Health Imaging Foundation Web Medical Imaging Framework To develop training materials, perform software maintenance, expand outreach, and provide community support for the Open Health Imaging Foundation (OHIF) web-based medical imaging framework including its underlying libraries (e.g., Cornerstone).

Enhancing the Open Source SciML Stack for Clinical Trial Simulations To make significant improvements to the SciML project, which is leveraged by pharmacologists in academia and industry for simulation of virtual clinical trials, drug design, and systems biology modeling.

Enhancing the Performance, Documentation, and Data Ecosystem for bedtools To enhance bedtools’ functionality, documentation, and access to data, which will empower and expand the user community.

Enhancing Usability of mixtools and tolerance for the Biomedical Community To provide significant modernization and enhanced usability of the R packages mixtools and tolerance for improved utilization and accessibility within the biomedical and health research communities.

Ensuring Reproducible Transcriptomic Analysis with DESeq2 and tximeta To extend DESeq2 functions to develop interfaces with Bioconductor’s rich experiment and annotation data, including single-cell datasets and genomic annotations, all leveraging tximeta’s metadata functionality for computational reproducibility.

Ensuring the Continued Growth of pandas To support continued maintenance and development of pandas, an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

Ensuring the Continued Growth of pandas To support the growth and health of pandas, the foundational library for tabular data structures in the Scientific Python Ecosystem, by funding continued maintenance and community building efforts.

EpiStan: Notebooks and Methods for Disease Modeling in Stan To build a repository of infectious disease models in Stan that will provide researchers with in-depth examples, helping them to draw sound conclusions and make better predictions from their data. ETE Toolkit - Enabling Large Scale Phylogenomic Analysis and Visualization To enable interactive analysis and exploration of phylogenetic data at the genomics and metagenomics scale.

ETE Toolkit: Phylogenomic Data Analysis and Visualization To support the release and maintenance of a new version of the ETE toolkit including updated documentation and new features such as tree diff, tree-like regular expression searches, and large tree visualization.

Expand Interoperability of Hosted Scientific Documentation To make scientific Python documentation more valuable by improving the user experience of linking between projects, and promote this ability within the scientific Python community.

Expanding and Deploying Data Visualization Tools for Mining Metagenomes To expand on existing web infrastructure by building highly intuitive and responsive data visualization tools for mining ‘shotgun’ metagenomic data.

Expanding and Modernizing the Salmon Ecosystem To expand the capabilities and improve the robustness and maintainability of the salmon software ecosystem, further widening its scope of applicability and improving the user and developer experience.

Expanding the Open mHealth Platform to Support Digital Biomarker Discovery Open mHealth created an open data standard and community for patient-generated data, and the Digital Biomarker Discovery Pipeline will enable transformation of that data into indicators of health outcomes and evaluation of novel digital biomarkers.

Extending Galaxy for Large-Scale and Integrative Biomedical Analyses To extend Galaxy, a web-based computational workbench used by thousands of scientists across the world, so that it can analyze large datasets and connect with other analysis tools.

Fast Software Package Management for Bio and Data Science To improve the tooling around the conda ecosystem to better serve the millions of users in biological sciences, data sciences, physics, robotics and other scientific disciplines.

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.

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.

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. Future: Simple, Scalable Parallelization in R for the Biomedical Community To sustain maintenance, improve community support, enhance usability and robustness, and add improvements for the future framework.

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.

GPU Acceleration, Rapid Releases, and Biomedical Examples for scikit-image To maintain the popular scikit-image Python library for microscopy and medical imaging data and bring significant improvements via development of a backend system enabling multi-threading and GPU acceleration, an improved release process for more rapid cycles, and expanded biomedical examples.

GPU-accelerated Computing in Bioconductor To support GPU-accelerated Bioconductor packages through continuous integration, user-friendly packaging of system-level dependencies, and foundational packages for Bioconductor GPU programming.

GPU-accelerating Fiji and Friends Using Distributed CLIJ, NEUBIAS-style To enable end-users of ImageJ/Fiji, Icy and napari to process biological imaging time-lapses or large-scale image data tile-by-tile on multiple graphics processing units (GPUs) using CLIJ.

Growing a Diverse and Inclusive Workflow Ecosystem with CWL To expand our community so new individuals can meaningfully contribute code, documentation, workflows and other software artifacts by hiring a dedicated software engineer.

GSVA: Optimizing Gene Set Variation Analysis for Single-Cell Data To optimize GSVA functionality to analyze single-cell and spatial transcriptomic data sets, increasing its robustness and scalability and improving user interface and documentation.

Sustainable computational biology training for LMICs in Africa To build a sustainable computational biology training infrastructure with accredited trainers, access to high quality training materials, and support for regional communities of trainees in low and middle income countries (LMICs) in Africa.

HTSJDK: Enhancing the Java Toolkit for Emerging Sequencing Technologies To enhance the HTSJDK Java toolkit for genomics with an extensible plugin framework that will enable support for emerging technologies required by contemporary analysis methods, such as long reads, graph/circular references, and epigenetic modifications.

ilastik and Scientific Python Ecosystem: Deep Integration with Other Tools To integrate ilastik with napari and Dask, replacing the outdated internal viewer and task scheduler by modern, community-supported alternatives with the aim to reduce technical debt, engage with the community, and deliver a superior user experience for the bioimage analysis community.

ilastik: Faster and More User-Friendly Through Full Pyramid Support To enable multi-scale interactive machine learning on large datasets in ilastik through full exploitation of state-of-the-art pyramidal file formats and viewers, and extend functionality to other bioimage analysis tools.

ilastik: Future-Proof Through Stable APIs and Interoperability To make ilastik more interoperable and its results more reusable and reproducible through the development of Python APIs and general improvement of the third-party developer experience.

Improving Bokeh Figure Publication: SVG, LaTeX, and Maintenance To improve Bokeh in key areas that are relevant to bioscience research and to secure a solid foundation for long-term project health and sustainability by engaging in important maintenance and fostering new contributors.

Improving Computational Methods for High-throughput Sequence Data Analysis To maintain and improve the three proposed software projects: minimap2, BWA and hifiasm, and extend them to new architectures and new data types. 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.

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.

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. Improving the Analytical Flexibility of bedtools To improve the flexibility and utility of bedtools for large-scale genomic analyses.

Improving Usability and Sustainability for NumPy and OpenBLAS To improve the robustness and usability of NumPy by continuing to work in documentation and community building, modernizing its integration with Fortran tools via numpy. f2py, and ensuring the sustainability of both NumPy and OpenBLAS.

Improving Usability of Core Neuroscience Analysis Tools with MNE-Python To enhance usability of MNE-Python through improvements to its computational efficiency, API, interactive visualization capabilities, and the clarity and consistency of documentation.

Improving User Experience and Debuggability of pip For All Python Users To complete the design, implementation, and rollout of pip's next-generation dependency resolver, and permanently improve pip's maintainer capacity and user experience.

Improving User Experience and Engagement for UCSC Xena To improve the user experience of UCSC Xena and better engage users by implementing the redesign of two core features using UX principles, standardizing training materials, and publishing a blog highlighting research use cases.

Inclusive and Accessible Scientific Computing in the Jupyter Ecosystem To bring systematically marginalized voices of disabled scientists into scientific computing communities via building and applying accessibility tools, standards, and community contribution practices in the Jupyter ecosystem.

Industry Open Source Diversity Genomics Internship Program To improve diversity of computational biology and open source development, providing professional industry opportunities for talent underrepresented within the field of genomics.

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.

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.

A collaborative interactive computing service model for global communities Education & Capacity Building To support a project that will enable collaboration, scalable analysis, and open workflows for communities in the Global South via community-focused interactive computing hubs in the cloud, paired with training and capacity building.

Invest in Open Infrastructure A non-profit initiative dedicated to helping focus investments in the open technology on which research and scholarship rely. IQ-TREE for Ultra-Large Genomic Data To develop an open standard and API for phylogenetic models and improve the speed and scalability of the IQ-TREE software for phylogenetic inference from ultra-large genomic data.

JupyterHub Community Strategic Lead To broaden participation in the JupyterHub community by establishing a role dedicated to strategy and stewardship for pathways into and throughout the community, as well as programs that provide onboarding and mentorship for historically underrepresented groups. JupyterHub Contributor in Residence Program To improve community support and technical maintenance across the JupyterHub repositories.

LinkML: An Open Data Modeling Framework to increase usability of LinkML (Linked data Modeling Language), an open, extensible framework for modeling, validating, and distributing data that is reusable and interoperable. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

MACS3, Peak Caller with Single-Cell Resolution To maintain the established infrastructure and optimize the current features of the popular peak caller MACS for gene regulation studies, while focusing on building the data structure and features for single-cell data analysis.

MACS3: A Versatile Peak Caller for Gene Regulation Studies To enhance the infrastructure to support the continuous development and growing community of the popular algorithm MACS for gene regulation studies, in order to expand its features and adapt to new technologies such as single-cell ATAC-seq.

Maintaining Rocker: Sustainability for Containerized Reproducible Analyses To put Rocker, the de facto standard for reproducible, containerized R analyses, on a path to sustainable maintenance through refactoring, improving the quality of documentation, expanding the community, and targeting new hardware platforms.

Maintenance & Extension of scikit-learn: Machine Learning in Python To further the sustainability and usability of scikit-learn by reducing the maintenance backlog and extending its machine learning models and pipelines to support more complex datasets.

Maintenance and Improvement of Validated, Community Developed NGS Analyses To improve the bcbio-nextgen toolkit, focusing on maintaining existing variant calling functionality and extending support for structural and RNA-seq variant analyses.

Matplotlib: Foundation of Scientific Visualization in Python To enable Matplotlib to continue as the core plotting library of the scientific Python ecosystem by addressing the maintenance backlog and planning Matplotlib's evolution to meet the community’s visualization challenges for the next decade.

Matplotlib: Foundation of Scientific Visualization in Python To enable Matplotlib to continue as the core plotting library of the scientific Python ecosystem for researchers in biomedical imaging, microscopy, and genomics by addressing the maintenance backlog and beginning Matplotlib's evolution to meet the community’s visualization challenges for the next decade.

Matplotlib: Foundation of Scientific Visualization in Python To support the continued maintenance, growth, development, and community engagement of Matplotlib, the foundational plotting library of the Scientific Python Ecosystem.

MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science To improve and maintain high-performance tools for analysis of biological systems at the molecular scale and incentivize scientists to drive transparent and reproducible research. MDAnalysis: Outreach and Project Manager To grow the MDAnalysis community sustainably.

Education & Capacity Building MetaDocencia provides online computational and scientific training to Spanish-speaking researchers, teachers, and professionals throughout Latin America.

MetaInsight and CINeMA: Reproducible Evidence for Clinical Decision-Making to develop the first user-friendly, open source software that synthesizes and evaluates the evidence about the effectiveness and safety of medical interventions and informs treatment decision-making. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6. MicroManager 2.

0: An Open Platform for Microscopy Image Acquisition To support the open source µManager optical microscopy acquisition platform to improve its architecture, infrastructure, and support to ensure many years of growth, both in user base and capabilities.

Migrating Protege to a Modern Web Stack To construct a solid foundation for the next generation of Protege using a modern web stack that will make Protege easier to maintain, extend, and — crucially — make it easier for third parties to contribute to the code base. Modernizing the igraph Interfaces To modernize the igraph interfaces to make network analysis easier.

Molecular Visualization: Transitioning Chimera to ChimeraX To keep ChimeraX molecular and microscopy analysis software current with the latest technology and facilitate the migration of tens of thousands of Chimera users to ChimeraX.

MSstats and Cardinal: Next Generation Statistical Mass Spectrometry in R To provide open-source, interoperable, and extensible statistical software for quantitative mass spectrometry, which enables experimentalists and developers of statistical methods to rapidly respond to changes in the evolving biotechnological landscape.

Neurodesk: a platform for reproducible neuroimaging To develop features for an improved user and developer experience in the Neurodesk platform allowing for easier, portable, scalable, and reproducible neuroscience and biomedical imaging analysis. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Next Generation File Formats for BioImaging To support the Bio-Formats user community and develop new formats to make proprietary file formats obsolete. Next Generation Mass Spectrometry with OpenMS To enable the analysis of thousands of next generation data-independent acquisition (DIA) mass spectrometry measurements by implementing algorithms, visualization tools, and cloud containers based on OpenMS and the OpenSWATH algorithm.

Next-Generation Movement Monitoring with the DeepLabCut Ecosystem To enhance the DeepLabCut ecosystem with a new 3D pose module, integration with generative AI (AmadeusGPT), providing codebase and DLC-Live! code upkeep, and continuing our DEI AI Residency Program. Note: This proposal was funded by The Kavli Foundation as part of our co-funded EOSS Cycle 6.

Next-Generation Simulation and Learning in Imaging-Based Biomedicine To develop and integrate open computational geometry and simulation technology enabling digital twins in biomedicine – next-generation imaging-based modeling, simulation, optimization, and learning. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

To keep the current momentum of initiatives and push forward with new actions for accessibility, internationalization, mentorships and ambassadors. Nextflow and nf-core: Reproducible Workflows for the Scientific Community To support a fast-growing, community-building software for infrastructure agnostic, open source biomedical pipelines.

Nextflow and nf-core: Reproducible Workflows for the Scientific Community To continue support for a fast-growing community, building open source software for infrastructure agnostic, open source biomedical analysis workflows. NGFF: Democratize Access to Next-Generation Bioimaging Data To coordinate and foster next-generation file formats while increasing community access to public imaging data.

NiPreps - a Community Framework for Reproducible Neuroimaging To solidify NiPreps by boosting community growth, securing maintenance, and developing new components to expand the diversity of supported data such as imaging parameters, modalities, populations, and species.

OME-Zarr Support for Java/Fiji To develop a general-purpose Java library for the community standard image file format OME-Zarr, and robustly integrate it into the widespread image processing and analysis software Fiji.

Ontological Resource Tagging and Discovery for Bioconductor To enhance discoverability and use of Bioconductor packages and data and teaching resources by tagging them with formal vocabulary and concept relations in ontologies like EDAM. Open Health Imaging Foundation (OHIF) and Cornerstone Medical Web Viewer To partner with hack.

diversity to serve as curriculum designers and mentors, equipping their Fellows to contribute to open source web-based medical imaging,