Online tutorial (10)#

Creating Workflows and Advanced Workflow Options#

Licensed CC-BY-4.0

Tags: Workflow

Content type: Tutorial, Online Tutorial

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


Data Stewardship Wizard#

Licensed UNKOWN

Leading open-source platform for collaborative and living data management plans.

Tags: Data Stewardship, Open Source, Research Data Management, FAIR-Principles

Content type: Website, Online Tutorial

https://ds-wizard.org/


Data life cycle#

ELIXIR (2021) Research Data Management Kit

Licensed CC-BY-4.0

In this section, information is organised according to the stages of the research data life cycle.

Tags: Data Life Cycle, Research Data Management

Content type: Collection, Website, Online Tutorial

https://rdmkit.elixir-europe.org/data_life_cycle


EPFLx: Image Processing and Analysis for Life Scientists#

Licensed ALL RIGHTS RESERVED

Tags: Bioimage Analysis

Content type: Online Tutorial

https://www.edx.org/learn/image-analysis/ecole-polytechnique-federale-de-lausanne-image-processing-and-analysis-for-life-scientists


Fiji#

Licensed BSD-2-CLAUSE

Fiji is a popular free open-source image processing package based on ImageJ.

Tags: Imagej, OMERO

Content type: Online Tutorial

https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html


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 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


Methods in bioimage analysis#

Christian Tischer

Licensed CC-BY-4.0

Tags: Bioimage Analysis

Content type: Online Tutorial, Video, Slide

https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/

https://doi.org/10.6019/TOL.BioImageAnalysis22-w.2022.00001.1

https://drive.google.com/file/d/1MhuqfKhZcYu3bchWMqogIybKjamU5Msg/view


OMERO - QuPath#

Rémy Jean Daniel Dornier

Licensed [‘CC-BY-NC-SA-4.0’]

OMERO-RAW extension for QuPath allows to directly access to the raw pixels of images. All types of images (RGB, fluorescence, …) are supported with this extension.

Tags: Bioimage Analysis, OMERO

Content type: Online Tutorial

https://wiki-biop.epfl.ch/en/data-management/omero/qupath


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

https://rdmorganiser.github.io/