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Workshops and courses
Microscopy data analysis: machine learning and the BioImage Archive
16 - 20 March 2026
Online
Machine learning Bioimaging Image analysis Bioimage analysis Machine learning models Scientific computing Light microscopy Electron microscopy -
Workshops and courses
Microscopy image analysis using Python
21 - 22 April 2026
Leuven, Belgium
Face-to-face
imaging
Showing 30 materials
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Recorded webinar
Methods in bioimage analysis
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Recorded webinar
Building a spatial transcriptomics platform
Transcriptomics Imaging Light microscopy Omics
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slides
Contribute to the BioImage.IO models
• beginnerImaging Image analysis using Deep Learning bioimageio image analysis -
slides
Welcome to the BioImage Model Zoo
• beginnerImaging Image analysis using Deep Learning bioimageio image analysis -
slides
BioImage Model Zoo: Advanced models in one-click
• beginnerImaging Image analysis using Deep Learning bioimageio image analysis -
slides
Nucleoli Segmentation <br> & <br> Feature Extraction <br> using CellProfiler
• beginnerImaging -
e-learning
FAIR Bioimage Metadata
• beginnerImaging Bioimaging Data management FAIR Data, Workflows, and Research Metadata -
e-learning
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
• beginnerImaging Bioimaging Data management FAIR Data, Workflows, and Research Metadata -
e-learning
Using BioImage.IO models for image analysis in Galaxy
•• intermediateImaging Deep learning Image annotation Image segmentation -
e-learning
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
•• intermediateImaging Data handling Data management Data sharing -
e-learning
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
• beginnerImaging Parameter optimisation Validation -
e-learning
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines
• beginnerImaging IDR dataset Overlay Rasterisation Spot detection -
e-learning
Introduction to Image Analysis using Galaxy
• beginnerImaging Conversion Image segmentation Object counting Overlay -
e-learning
Object tracking using CellProfiler
•• intermediateImaging Isolated object tracking Multi-channel image -
e-learning
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
•• intermediateImaging Conversion Multi-channel image Object feature extraction ROI selection -
e-learning
Nucleoli segmentation and feature extraction using CellProfiler
•• intermediateImaging Image segmentation Multi-channel image Object feature extraction -
e-learning
Voronoi segmentation
•• intermediateImaging Image segmentation Multi-channel image Object counting Overlay Tessellation -
e-learning
Tracking of mitochondria and capturing mitoflashes
•• intermediateImaging Isolated object tracking Temporal analysis Time-lapse data -
e-learning
Training Custom YOLO Models for Segmentation of Bioimages
•• intermediateImaging Deep learning Image annotation Image segmentation -
e-learning
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
•• intermediateImaging Image segmentation Tissue imaging -
e-learning
Analyse HeLa fluorescence siRNA screen
•• intermediateImaging Fluorescence microscopy High-throughput screening Image segmentation Image thresholding Object feature extraction -
Recorded webinar
Open FAIR data: the role of public data archives
Imaging
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Recorded webinar
The BioImage Archive: Home for life sciences microscopy data
Bioimaging Imaging
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Recorded webinar
Developing community resources for bioimage analysis training
Imaging Bioimaging
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Recorded webinar
Visualising integrated single cell and spatial transcriptomics datasets
Transcriptomics Imaging Omics
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hands-on tutorial
Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
• beginnerData management Imaging REMBI -
e-learning
EMPIAR: Quick tour
Electron microscopy Image archive Bioimaging Microscopy
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e-learning
Structural volume data
Electron microscopy Protein structure analysis Structural biology Structural bioinformatics Segmentation Volume matching
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Slides
Life Science RDM 2023 Course - Extended version in 6 modules
• beginnerData management FAIR data Biology Genomics Imaging Proteomics Bioinformatics Biodiversity Data Management Plan Data management planning … -
Open educational resource, Training materials
I3D:bio's OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training
• beginnerOMERO Research Data Management REMBI Microscopy data Metadata I3D:bio RDM4mic data organisation