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 single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines
RNA smFISH bioimaging
Tracking of mitochondria and capturing mitoflashes
bioimaging mitoflash mitochondria
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

Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoRiccardo Massei avatar Riccardo Masseiorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoKrzysztof Poterlowicz avatar Krzysztof PoterlowiczJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoJulia Jakiela avatar Julia Jakielaorcid logoArmin Dadras avatar Armin DadrasYi Sun avatar Yi Sunorcid logoMartin Čech avatar Martin Čechorcid logoThomas Wollmann avatar Thomas Wollmannorcid logoEven Moa Myklebust avatar Even Moa Myklebustorcid logoCameron Watson avatar Cameron Watsonorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoHelena Rasche avatar Helena RascheAnup Kumar avatar Anup Kumarorcid logoAllison Creason avatar Allison Creasonorcid logoAnne Fouilloux avatar Anne FouillouxLaura Cooper avatar Laura Cooper

Funding

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

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de.NBI
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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.
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ELIXIR Europe
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UFR
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NFDI4Bioimage
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DFG

References