Imaging — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoLeonid Kostrykin avatar Leonid Kostrykinorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
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Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.
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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
FAIR Bioimage Metadata ✅ ✅ ✅ ❌
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data ✅ ✅ ✅ ❌
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 ✅ ✅
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 ✅ ✅
Use Pycytominer in Galaxy for processing high dimensional image-based readouts ✅ ✅ ✅
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' Oct 25, 2026 6 ✅ ❌ ❌
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 2024_OMERO_Basic_Upload Oct 25, 2026 1 ❌ ✅ ✅
Analyse HeLa fluorescence siRNA screen analyze_screen Oct 25, 2026 6 ✅ ❌ ❌
Analyse HeLa fluorescence siRNA screen feature_extraction Oct 25, 2026 6 ✅ ❌ ❌
End-to-End Tissue Microarray Image Analysis with Galaxy-ME GTN_Exemplar_002_TMA_workflow_Feb2025 Oct 25, 2026 1 ✅ ❌ ❌
Nucleoli segmentation and feature extraction using CellProfiler CP_pipeline_IDR_training Oct 25, 2026 3 ❌ ❌ ❌
Object tracking using CellProfiler CP_object_tracking_example Oct 25, 2026 1 ❌ ❌ ❌
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Electrophoresis-Gel-Bands-Image-Analysis Oct 25, 2026 1 ❌ ✅ ❌
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 2025_2D_spot_detection Oct 25, 2026 1 ✅ ✅ ✅
Quantitative Analysis of Histological Staining Using Color Deconvolution Histological Staining Area Quantification Oct 25, 2026 1 ✅ ✅ ✅
Segmentation of Anatomical Structures in Medical 3-D Images Segmentation of Anatomical Structures in Medical Images Oct 25, 2026 1 ✅ ✅ ✅
Tracking of mitochondria and capturing mitoflashes Capturing mitoflashes Oct 25, 2026 1 ✅ ✅ ❌
Use Pycytominer in Galaxy for processing high dimensional image-based readouts pycitominer-training Oct 25, 2026 1 ✅ ✅ ❌
Using BioImage.IO models for image analysis in Galaxy Image prediction with BioImage.IO model (imported from uploaded file) Oct 25, 2026 3 ✅ ✅ ✅
Voronoi segmentation Voronoi segmentation Oct 25, 2026 1 ✅ ✅ ✅
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM ISCC - image analysis workflow example Oct 25, 2026 1 ✅ ✅ ❌
Execute a BiaPy workflow in Galaxy BiaPy Oct 25, 2026 1 ✅ ✅ ✅
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Segmentation_Values_Testing Oct 25, 2026 1 ✅ ✅ ✅
Training Custom YOLO Models for Segmentation of Bioimages YOLO training and segmentation workflow Oct 25, 2026 1 ❌ ✅ ❌

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