Imaging

Image analysis using Galaxy

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.
Lesson Slides Hands-on Recordings Input dataset Workflows
Analyse HeLa fluorescence siRNA screen
HeLa
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
Introduction to Image Analysis using Galaxy
HeLa
Nucleoli segmentation and feature extraction using CellProfiler
Object tracking using CellProfiler
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
bioimaging
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
RNA DNA Protein bioimaging
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines
RNA smFISH bioimaging
Tracking of mitochondria and capturing mitoflashes
bioimaging mitoflash mitochondria
Training Custom YOLO Models for Segmentation of Bioimages
Using BioImage.IO models for image analysis in Galaxy
bioimaging AI
Voronoi segmentation
imageanalysis segmentation voronoi
FAIR Bioimage Metadata
fair data management bioimaging
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
fair data management bioimaging

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano

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Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoJulia Jakiela avatar Julia Jakielaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoRiccardo Massei avatar Riccardo Masseiorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoKrzysztof Poterlowicz avatar Krzysztof PoterlowiczJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoMartin Čech avatar Martin ČechAnup Kumar avatar Anup Kumarorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoLaura Cooper avatar Laura Cooperorcid logoAllison Creason avatar Allison Creasonorcid logoThomas Wollmann avatar Thomas WollmannYi Sun avatar Yi Sunorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoKatarzyna Kamieniecka avatar Katarzyna KamienieckaArif ul Maula Khan avatar Arif ul Maula Khanorcid logoEven Moa Myklebust avatar Even Moa Myklebustorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoCameron Watson avatar Cameron Watsonorcid logoArmin Dadras avatar Armin Dadrasorcid logoHelena Rasche avatar Helena RascheReyhaneh Tavakoli avatar Reyhaneh Tavakoli

Funding

These individuals or organisations provided funding support for the development of this resource

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DFG
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de.NBI
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ELIXIR Europe
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UFR
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OSCARS-FIESTA
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OSCARS
The OSCARS project has received funding from the European Commission’s Horizon Europe Research and Innovation programme under grant agreement No. 101129751
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NFDI4Bioimage
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DASH UK
This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.

References