Workflow (9)#
BIOMERO - A scalable and extensible image analysis framework#
Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A.J. Reits, Ron A. Hoebe, Przemek M. Krawczyk
Published None
Licensed CC-BY-4.0
The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments.
Tags: OMERO, Workflow, Bioimage Analysis
Content type: Publication
Creating Workflows and Advanced Workflow Options#
Licensed CC-BY-4.0
Tags: Workflow
Content type: Tutorial, Online Tutorial
Galaxy workflows#
Licensed CC0-1.0
A workflow is a chain of analysis steps. In Galaxy, we can create a workflow from an existing analysis history, or we can create one visually by adding tools to a canvas. This tutorial covers building a workflow to analyse a bacterial genome, from input FASTQ sequencing reads to assembly, annotation, and visualization.
Tags: Workflow
Content type: Online Tutorial, Tutorial
https://galaxy-au-training.github.io/tutorials/modules/workflows/
KNIME Image Processing#
None
Licensed GPL-3.0
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, Workflow
Content type: Tutorial, Online Tutorial, Documentation
Multimodal large language models for bioimage analysis#
Shanghang Zhang, Gaole Dai, Tiejun Huang, Jianxu Chen
Licensed CC-BY-NC-SA
Multimodal large language models have been recognized as a historical milestone in the field of artificial intelligence and have demonstrated revolutionary potentials not only in commercial applications, but also for many scientific fields. Here we give a brief overview of multimodal large language models through the lens of bioimage analysis and discuss how we could build these models as a community to facilitate biology research
Tags: Bioimage Analysis, FAIR-Principles, Workflow
Content type: Publication
User friendly Image metadata annotation tool/workflow for OMERO#
Jens Wendt
Tags: Metadata, Workflow, OMERO
Content type: Forum Post
https://forum.image.sc/t/user-friendly-image-metadata-annotation-tool-workflow-for-omero/87925/1
WorkflowHub#
Stian Soiland-Reyes, Finn Bacall, Bert Droesbeke, Alan R Williams, Johan Gustafsson, et al.
Licensed BSD-3-CLAUSE
A registry for describing, sharing and publishing scientific computational workflows.
Tags: Bioinformatics, Workflow, Workflow Engine, Python, R
Content type: Collection
cba-support-template#
Arif Khan, Christian Tischer, Sebastian Gonzalez, Dominik Kutra, Felix Schneider, et al.
Published 2021-12-01
Licensed MIT
Tags: Workflow, Research Data Management
Content type: Tutorial
nextflow-workshop#
Tuur Muyldermans, Kris Davie, Alexander, Nicolas Vannieuwkerke, Kobe Lavaerts, Marcel Ribeiro-Dantas, Bruna Piereck, Steff Taelman
Published 2023-03-29T10:40:04+00:00
Licensed CC-BY-4.0
Nextflow workshop materials March 2023
Tags: Workflow, Nextflow
Content type: Github Repository, Tutorial