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

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.

Follow topic updates with our RSS Feed

Community Resources

Community Home Maintainer Home

Editorial Board

This material is reviewed by our Editorial Board:

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

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

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

Funding

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

Logo
OSCARS
The OSCARS project has received funding from the European Commission’s Horizon Europe Research and Innovation programme under grant agreement No. 101129751
Logo
OSCARS-FIESTA
Logo
de.NBI
Logo
NFDI4Bioimage
Logo
UFR
Logo
ELIXIR Europe
Logo
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.
Logo
DFG

References