Workflow (10)#

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, Image Data Management

Content type: Publication

https://doi.org/10.1016/j.patter.2024.101024


Creating Workflows and Advanced Workflow Options#

Licensed CC-BY-4.0

Tags: Workflow

Content type: Tutorial, Online Tutorial

https://galaxyproject.org/learn/advanced-workflow/


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/


I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library#

Stephane Rigaud, Robert Haase

Licensed BSD-3-CLAUSE

Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline.

Tags: Clesperanto, Training, Bioimage Analysis, Notebooks, Workflow

Content type: Github Repository, Workshop, Tutorial, Notebook

StRigaud/clesperanto_workshop_I2K24


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

https://www.knime.com/community/image-processing


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, Large Language Models, FAIR-Principles, Workflow

Content type: Publication

https://www.nature.com/articles/s41592-024-02334-2

https://arxiv.org/abs/2407.19778


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

https://workflowhub.eu/


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

https://git.embl.de/grp-cba/cba-support-template


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

vibbits/nextflow-workshop

https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/nextflow-workshop/main/README.md#1