Documentation (14)#
AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources#
[‘Caterina Fuster-Barceló’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Workflow Engine, Bio-Image Analysis
Content type: Documentation
BiaPy: Bioimage analysis pipelines in Python#
[‘Daniel Franco-Barranco’, ‘et al.’]
BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.
Tags: Workflow Engine, Python
Content type: Documentation
BioEngine Documentation#
[‘Wei Ouyang’, ‘Nanguage’, ‘Jeremy Metz’, ‘Craig Russell’]
Licensed MIT
BioEngine, a Python package designed for flexible deployment and execution of bioimage analysis models and workflows using AI, accessible via HTTP API and RPC.
Tags: Workflow Engine, Deep Learning, Python
Content type: Documentation
Fractal Documentation#
Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
Tags: Workflow Engine, Python
Content type: Documentation
Galaxy Documentation#
Galaxy is an open source, web-based platform for data intensive biomedical research.
Tags: Workflow Engine
Content type: Documentation
JIPipe: visual batch processing for ImageJ#
[‘Ruman Gerst’, ‘Zoltán Cseresnyés’, ‘Marc Thilo Figge’]
JIPipe is an open-source visual programming language for easy-access pipeline development
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
Making your package available on conda-forge#
[‘Kevin Yamauchi’]
Licensed CC-BY-4.0
Tags: Deployment, Python
Content type: Documentation
https://kevinyamauchi.github.io/open-image-data/how_tos/conda_forge_packaging.html
MiToBo - A Toolbox for Image Processing and Analysis#
[‘Birgit Möller’, ‘Markus Glaß’, ‘Danny Misiak’, ‘Stefan Posch’]
The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103
ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#
[‘Stephen J. Cross’, ‘Jordan D. J. R. Fisher’, ‘Mark A. Jepson’]
ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#
[‘Mohamed M. Abdrabbou’, ‘Mehrnaz Babaki’, ‘Tom Boissonnet’, ‘Michele Bortolomeazzi’, ‘Eik Dahms’, ‘Vanessa A. F. Fuchs’, ‘Moritz Hoevels’, ‘Niraj Kandpal’, ‘Christoph Möhl’, ‘Joshua A. Moore’, ‘Astrid Schauss’, ‘Andrea Schrader’, ‘Torsten Stöter’, ‘Julia Thönnißen’, ‘Monica Valencia-S.’, ‘H. Lukas Weil’, ‘Jens Wendt and Peter Zentis’]
Licensed CC-BY-4.0
Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, Omero, Python, Research Data Management
Content type: Event, Publication, Documentation
NextFlow documentation#
Nextflow enables scalable and reproducible scientific workflows using software containers.
Tags: Workflow Engine
Content type: Documentation
OME Documentation#
Licensed CC-BY-4.0
Tags: Omero
Content type: Documentation
OMERO documentation#
Licensed UNKNOWN
Tags: Omero
Content type: Documentation
Snakemake Documentation#
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
Tags: Workflow Engine, Python
Content type: Documentation
https://snakemake.readthedocs.io/en/stable/
https://academic.oup.com/bioinformatics/article/28/19/2520/290322