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
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:

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

Funding

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

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

References