Documentation (19)#
AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources#
Caterina Fuster-Barceló
Licensed UNKNOWN
Tags: Artificial Intelligence, Workflow Engine, Bioimage 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
BioFormats Command line (CLI) tools#
Published 2024-10-24
Licensed CC-BY-4.0
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. There are several scripts for using Bio-Formats on the command line, which are listed here.
Tags: Bioimage Data
Content type: Documentation
https://bio-formats.readthedocs.io/en/v8.0.0/users/comlinetools/index.html
Dokumentation und Anleitung zum elektronischen Laborbuch (eLabFTW)#
Lienhard Wegewitz, F. Strauß
Published 2020-03-23
Licensed AGPL-3.0
Documentation for eLabFTW. With eLabFTW you get a secure, modern and compliant system to track your experiments efficiently but also manage your lab with a powerful and versatile database.
Tags: Research Data Management
Content type: Documentation, Document, Tutorial
https://www.fdm.tu-clausthal.de/fileadmin/FDM/documents/Manual_eLab_v0.3_20200323.pdf
Example Pipeline Tutorial#
Tim Monko
Published 2024-10-28
Licensed BSD-3-CLAUSE
Napari-ndev is a collection of widgets intended to serve any person seeking to process microscopy images from start to finish. The goal of this example pipeline is to get the user familiar with working with napari-ndev for batch processing and reproducibility (view Image Utilities and Workflow Widget).
Tags: Napari, Microscopy Image Analysis, Bioimage Analysis
Content type: Documentation, Github Repository, Tutorial
https://timmonko.github.io/napari-ndev/tutorial/01_example_pipeline/
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
KNIME Image Processing#
None
Licensed GPLV3
The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME.
Tags: Imagej, OMERO, Bioimage Data, Workflow
Content type: Tutorial, Online Tutorial, Documentation
Key-Value pairs scripts#
Licensed UNKNOWN
The key-value pairs are annotations in OMERO useful to describe thoroughly the data and can be added & edited via the OMERO.web interface.
Tags: OMERO
Content type: Documentation, Collection
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