Open source software (7)#
Insights and Impact From Five Cycles of Essential Open Source Software for Science#
Kate Hertweck, Carly Strasser, Dario Taraborelli
Licensed CC-BY-4.0
Open source software (OSS) is essential for advancing scientific discovery, particularly in biomedical research, yet funding to support these vital tools has been limited. The Chan Zuckerberg Initiative’s Essential Open Source Software for Science (EOSS) program has significantly contributed to this field by providing $51.8 million in funding over five years to support the maintenance, growth, and community engagement of critical OSS tools. The program has impacted scientific OSS projects by improving their technical outputs, community building, and sustainability practices, and fostering collaborations within the OSS community. Additionally, EOSS funding has enhanced diversity, equity, and inclusion within the OSS community, although changes in principal investigator demographics were not observed. The funded projects have had a substantial impact on biomedical research by improving the usability and accessibility of scientific software, which has led to increased adoption and advancements in various biomedical fields.
Tags: Open Source Software, Funding, Sustainability
Content type: Publication
NGFF Converter#
Licensed GPL-2.0
An easy to use and open source converter for bioimaging data. NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF.
Tags: Bioimage Data, Open Source Software
Content type: Application
Open Micoscropy Environment (OME) Youtube Channel#
Published None
Licensed CC-BY-4.0
OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data
Tags: Open Source Software, Microscopy Image Analysis, Bioimage Data
Content type: Video, Collection
QuPath for Python programmers#
Alan O’Callaghan, Léo Leplat
Published 2024-10-23
Licensed UNKNOWN
These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop.
Tags: Python, Notebooks, Open Source Software, Bioimage Analysis
Content type: Github Repository, Notebook, Collection
RDMO - Research Data Management Organiser#
Licensed UNKNOWN
Der Research Data Management Organiser (RDMO) unterstützt Forschungsprojekte bei der Planung, Umsetzung und Verwaltung aller Aufgaben des Forschungsdatenmanagements.
Tags: Research Data Management, Open Source Software
Content type: Website, Online Tutorial
bioformats2raw Converter#
Melissa Linkert, Chris Allan, Josh Moore, Sébastien Besson, David Gault, et al.
Licensed GPL-2.0
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
raw2ometiff Converter#
Melissa Linkert, Chris Allan, Sébastien Besson, Josh Moore
Licensed GPL-2.0
Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository