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.

Introduction

Start here if you are new to Image Analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Image Analysis using Galaxy
Image segmentation Conversion Object counting Overlay
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
Data management Data handling Data sharing
FAIR Bioimage Metadata
Data management Metadata Bioimaging
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
Data management Metadata Bioimaging

Analyses

These tutorials will help you analyse your image data

Lesson Slides Hands-on Recordings Input dataset Workflows
Analyse HeLa fluorescence siRNA screen
Image segmentation Object feature extraction Image thresholding High-throughput screening Fluorescence microscopy
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
Image segmentation Tissue imaging
Nucleoli segmentation and feature extraction using CellProfiler
Image segmentation Object feature extraction Multi-channel image
Object tracking using CellProfiler
Isolated object tracking Multi-channel image
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
ROI selection Conversion Object feature extraction Multi-channel image
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines
IDR dataset Spot detection Rasterisation Overlay
Tracking of mitochondria and capturing mitoflashes
Isolated object tracking Temporal analysis Time-lapse data
Using BioImage.IO models for image analysis in Galaxy
Image segmentation Image annotation Deep learning
Voronoi segmentation
Tessellation Image segmentation Object counting Overlay Multi-channel image

Advanced topics

Tutorials covering advanced topics

Lesson Slides Hands-on Recordings Input dataset Workflows
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
Parameter optimisation Validation
Training Custom YOLO Models for Segmentation of Bioimages
Image segmentation Image annotation Deep learning

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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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 logoThomas Wollmann avatar Thomas Wollmannorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoRiccardo Massei avatar Riccardo MasseiArif ul Maula Khan avatar Arif ul Maula Khanorcid logoPaul De Geest avatar Paul De GeestReyhaneh Tavakoli avatar Reyhaneh Tavakoliorcid logoHelena Rasche avatar Helena Rascheorcid logoCameron Watson avatar Cameron Watsonorcid logoBjörn Grüning avatar Björn Grüningorcid logoEven Moa Myklebust avatar Even Moa Myklebustorcid logoMartin Čech avatar Martin Čechorcid logoSaskia Hiltemann avatar Saskia HiltemannAnup Kumar avatar Anup Kumarorcid logoAllison Creason avatar Allison Creasonorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoAnne Fouilloux avatar Anne FouillouxYi Sun avatar Yi SunLaura Cooper avatar Laura Cooperorcid logoJulia Jakiela avatar Julia Jakielaorcid logoArmin Dadras avatar Armin DadrasJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoKhaled Jum'ah avatar Khaled Jum'ah

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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DFG
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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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OSCARS-FIESTA
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ELIXIR Europe
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UFR
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NFDI4Bioimage

References