imaging

Tutorials covering imaging

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Imaging

Lesson Slides Hands-on Recordings Input dataset Workflows
AI pipeline for annotating marine species (Project Moorev - Marine)
Marine ecosystems biodiversity AI segmentation YOLO deep learning object detection
Analyse HeLa fluorescence siRNA screen
Image segmentation Object feature extraction Image thresholding High-throughput screening Overlay Fluorescence microscopy
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM
Data management Data handling Data sharing Validation
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
Image segmentation Tissue imaging
Execute a BiaPy workflow in Galaxy
Image segmentation Image annotation Deep learning Conversion Overlay 3D image Volume rendering
Introduction to Image Analysis using Galaxy
Image segmentation Image thresholding Conversion Object counting Overlay Fluorescence microscopy
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 Earth observation
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
Data management Data handling Data sharing ROI selection
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
Image segmentation Parameter optimisation Validation
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
Quantitative Analysis of Histological Staining Using Color Deconvolution
Microscopy Bioimaging Histology pathology
Segmentation of Anatomical Structures in Medical 3-D Images
Image segmentation Conversion Overlay Object feature extraction Medical imaging Computed tomography 3D image Volume rendering
Tracking of mitochondria and capturing mitoflashes
Isolated object tracking Temporal analysis Time-lapse data
Training Custom YOLO Models for Segmentation of Bioimages
Image segmentation Image annotation Deep learning
Use Pycytominer in Galaxy for processing high dimensional image-based readouts
Object feature extraction high-throughput data cleaning cellprofiler deepprofiler
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
Where to start with bioimage analysis in Galaxy
Microscopy Bioimaging Histology

Metabolomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Mass spectrometry imaging: Examining the spatial distribution of analytes
metabolomics mass spectrometry imaging imaging
Mass spectrometry imaging: Finding differential analytes
metabolomics mass spectrometry imaging imaging

Proteomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Mass spectrometry imaging: Loading and exploring MSI data
mouse imaging mass spectrometry imaging

Contributors

This material was contributed to by:

orcid logoMartin Etzrodt avatar Martin Etzrodtorcid logoHelena Rasche avatar Helena Rascheorcid logoCameron Watson avatar Cameron Watsonorcid logoReyhaneh Tavakoli-Koopaei avatar Reyhaneh Tavakoli-KoopaeiEnis Afgan avatar Enis Afganorcid logoAllison Creason avatar Allison Creasonorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoThomas Wollmann avatar Thomas WollmannYi Sun avatar Yi Sunorcid logoBjörn Grüning avatar Björn GrüningErik Serrano avatar Erik SerranoJean-Karim Hériché avatar Jean-Karim Hérichéorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoEven Moa Myklebust avatar Even Moa Myklebustorcid logoMarie Josse avatar Marie Josseorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNadine Le Bris avatar Nadine Le BrisMaria Arrate Munoz Barrutia avatar Maria Arrate Munoz Barrutiaorcid logoAnne Fouilloux avatar Anne FouillouxMaren Stillger avatar Maren Stillgerorcid logoPavankumar Videm avatar Pavankumar VidemDaniel Franco Barranco avatar Daniel Franco Barrancoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMarius van den Beek avatar Marius van den Beekorcid logoAnup Kumar avatar Anup Kumarorcid logoMaarten Paul avatar Maarten Paulorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoMartin Čech avatar Martin Čechorcid logoMelanie Föll avatar Melanie Föllorcid logoRiccardo Massei avatar Riccardo MasseiArif ul Maula Khan avatar Arif ul Maula Khanorcid logoBérénice Batut avatar Bérénice Batutorcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoArmin Dadras avatar Armin DadrasKevin Payet avatar Kevin PayetArthur Barreau avatar Arthur BarreauDave Bunten avatar Dave BuntenSimon Bray avatar Simon Bray

Funding

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

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DFG
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MOOREV
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ELIXIR Europe
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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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PNDB
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ISYEB
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de.NBI
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UFR
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MNHN
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SU
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OSCARS-FIESTA
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NFDI4Bioimage
NFDI4BIOIMAGE is a nationwide community of researchers, imaging specialists and data experts who work with biological image data. We support anyone who generates, analyses or manages microscopy and bioimaging data. Our aim is to make imaging data easier to find, access, reuse and share by providing practical tools, clear guidance and hands on training. We collaborate closely with laboratories and research communities across Germany to understand their needs and develop solutions that help with real everyday challenges. Whether you are building new workflows, exploring advanced analysis methods or improving your data management, NFDI4BIOIMAGE offers support, expertise and a welcoming network.