Imaging — Editorial Board Home

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Editorial Board

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

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Image Analysis using Galaxy ✅ ✅ ✅
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy ✅ ✅
Where to start with bioimage analysis in Galaxy ✅ ✅
FAIR Bioimage Metadata ✅ ✅ ✅ ❌
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data ✅ ✅ ✅ ❌
Analyse HeLa fluorescence siRNA screen ✅ ✅ ✅ ✅
End-to-End Tissue Microarray Image Analysis with Galaxy-ME ✅ ✅
Nucleoli segmentation and feature extraction using CellProfiler ✅ ❌
Object tracking using CellProfiler ✅ ✅ ✅
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools ✅ ✅ ✅
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines ✅ ✅ ✅
Quantitative Analysis of Histological Staining Using Color Deconvolution ✅ ✅
Segmentation of Anatomical Structures in Medical 3-D Images ✅ ✅
Tracking of mitochondria and capturing mitoflashes ✅ ✅
Using BioImage.IO models for image analysis in Galaxy ✅ ✅
Voronoi segmentation ✅ ✅ ✅
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM ✅ ✅
Execute a BiaPy workflow in Galaxy ✅ ✅
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy ✅ ✅ ✅
Training Custom YOLO Models for Segmentation of Bioimages ❌ ✅
AI pipeline for annotating marine species (Project Moorev - Marine) ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Introduction to Image Analysis using Galaxy Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy' Aug 3, 2026 6 ✅ ❌ ❌
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 2024_OMERO_Basic_Upload Aug 3, 2026 1 ❌ ✅ ✅
Analyse HeLa fluorescence siRNA screen analyze_screen Aug 3, 2026 6 ✅ ❌ ❌
Analyse HeLa fluorescence siRNA screen feature_extraction Aug 3, 2026 6 ✅ ❌ ❌
End-to-End Tissue Microarray Image Analysis with Galaxy-ME GTN_Exemplar_002_TMA_workflow_Feb2025 Aug 3, 2026 1 ✅ ❌ ❌
Nucleoli segmentation and feature extraction using CellProfiler CP_pipeline_IDR_training Aug 3, 2026 3 ❌ ❌ ❌
Object tracking using CellProfiler CP_object_tracking_example Aug 3, 2026 1 ❌ ❌ ❌
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Electrophoresis-Gel-Bands-Image-Analysis Aug 3, 2026 1 ❌ ✅ ❌
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 2025_2D_spot_detection Aug 3, 2026 1 ✅ ✅ ✅
Quantitative Analysis of Histological Staining Using Color Deconvolution Histological Staining Area Quantification Aug 3, 2026 1 ✅ ✅ ✅
Segmentation of Anatomical Structures in Medical 3-D Images Segmentation of Anatomical Structures in Medical Images Aug 3, 2026 1 ✅ ✅ ✅
Tracking of mitochondria and capturing mitoflashes Capturing mitoflashes Aug 3, 2026 1 ✅ ✅ ❌
Using BioImage.IO models for image analysis in Galaxy Image prediction with BioImage.IO model (imported from uploaded file) Aug 3, 2026 3 ✅ ✅ ✅
Voronoi segmentation Voronoi segmentation Aug 3, 2026 1 ✅ ✅ ✅
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM ISCC - image analysis workflow example Aug 3, 2026 1 ✅ ✅ ❌
Execute a BiaPy workflow in Galaxy BiaPy Aug 3, 2026 1 ✅ ✅ ✅
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Segmentation_Values_Testing Aug 3, 2026 1 ✅ ✅ ✅
Training Custom YOLO Models for Segmentation of Bioimages YOLO training and segmentation workflow Aug 3, 2026 1 ❌ ✅ ❌

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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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