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 logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoDiana Chiang Jurado avatar Diana Chiang Jurado

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.
Sufficient Editorial Board Members Done ✅ (3 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
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Annotate Funders Done ✅ (13 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.
Review Feedback Received Ongoing 🔁 Review all feedback received for the Imaging topic and create GitHub issues or PRs where needed.
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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 10, 2026 6 ✅ ❌ ❌
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 2024_OMERO_Basic_Upload Oct 10, 2026 1 ❌ ✅ ✅
Analyse HeLa fluorescence siRNA screen analyze_screen Oct 10, 2026 6 ✅ ❌ ❌
Analyse HeLa fluorescence siRNA screen feature_extraction Oct 10, 2026 6 ✅ ❌ ❌
End-to-End Tissue Microarray Image Analysis with Galaxy-ME GTN_Exemplar_002_TMA_workflow_Feb2025 Oct 10, 2026 1 ✅ ❌ ❌
Nucleoli segmentation and feature extraction using CellProfiler CP_pipeline_IDR_training Oct 10, 2026 3 ❌ ❌ ❌
Object tracking using CellProfiler CP_object_tracking_example Oct 10, 2026 1 ❌ ❌ ❌
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Electrophoresis-Gel-Bands-Image-Analysis Oct 10, 2026 1 ❌ ✅ ❌
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 2025_2D_spot_detection Oct 10, 2026 1 ✅ ✅ ✅
Quantitative Analysis of Histological Staining Using Color Deconvolution Histological Staining Area Quantification Oct 10, 2026 1 ✅ ✅ ✅
Segmentation of Anatomical Structures in Medical 3-D Images Segmentation of Anatomical Structures in Medical Images Oct 10, 2026 1 ✅ ✅ ✅
Tracking of mitochondria and capturing mitoflashes Capturing mitoflashes Oct 10, 2026 1 ✅ ✅ ❌
Use Pycytominer in Galaxy for processing high dimensional image-based readouts pycitominer-training Oct 10, 2026 1 ✅ ✅ ❌
Using BioImage.IO models for image analysis in Galaxy Image prediction with BioImage.IO model (imported from uploaded file) Oct 10, 2026 3 ✅ ✅ ✅
Voronoi segmentation Voronoi segmentation Oct 10, 2026 1 ✅ ✅ ✅
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM ISCC - image analysis workflow example Oct 10, 2026 1 ✅ ✅ ❌
Execute a BiaPy workflow in Galaxy BiaPy Oct 10, 2026 1 ✅ ✅ ✅
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Segmentation_Values_Testing Oct 10, 2026 1 ✅ ✅ ✅
Training Custom YOLO Models for Segmentation of Bioimages YOLO training and segmentation workflow Oct 10, 2026 1 ❌ ✅ ❌

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