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 Object Detection and Segmentation in 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 logoAllison Creason avatar Allison Creasonorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoJulia Jakiela avatar Julia JakielaJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoEven Moa Myklebust avatar Even Moa Myklebustorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMartin Čech avatar Martin Čechorcid logoArmin Dadras avatar Armin Dadrasorcid logoAnne Fouilloux avatar Anne FouillouxAnup Kumar avatar Anup Kumarorcid logoBjörn Grüning avatar Björn Grüningorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoHelena Rasche avatar Helena RascheYi Sun avatar Yi Sunorcid logoRiccardo Massei avatar Riccardo Masseiorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCameron Watson avatar Cameron Watsonorcid logoThomas Wollmann avatar Thomas WollmannLaura Cooper avatar Laura CooperArif UI Maula Khan avatar Arif UI Maula Khan

Funding

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

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OSCARS-FIESTA
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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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UFR
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NFDI4Bioimage
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DFG
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de.NBI
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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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ELIXIR Europe

References