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-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.
Sufficient Editorial Board Members More required ❌ Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Pending ❌ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (6 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.

Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Analyse HeLa fluorescence siRNA screen ✅ ✅ ✅ ✅
End-to-End Tissue Microarray Image Analysis with Galaxy-ME ✅ ✅
Introduction to Image Analysis using Galaxy ✅ ✅ ✅
Nucleoli segmentation and feature extraction using CellProfiler ✅ ❌
Object tracking using CellProfiler ✅ ✅ ✅
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy ✅ ✅
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy ✅ ✅ ✅
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines ✅ ✅ ✅
Tracking of mitochondria and capturing mitoflashes ✅ ✅
Using BioImage.IO models for image analysis in Galaxy ✅ ✅
Voronoi segmentation ❌ ✅ ✅
FAIR Bioimage Metadata ✅ ✅ ✅ ❌
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data ✅ ✅ ✅ ❌

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Analyse HeLa fluorescence siRNA screen analyze_screen Jun 1, 2025 6 ✅ ❌ ❌
Analyse HeLa fluorescence siRNA screen feature_extraction Jun 1, 2025 6 ✅ ❌ ❌
End-to-End Tissue Microarray Image Analysis with Galaxy-ME GTN_Exemplar_002_TMA_workflow_Feb2025 Jun 1, 2025 1 ✅ ❌ ❌
Introduction to Image Analysis using Galaxy Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy' Jun 1, 2025 6 ✅ ❌ ❌
Nucleoli segmentation and feature extraction using CellProfiler CP_pipeline_IDR_training Jun 1, 2025 3 ❌ ❌ ❌
Object tracking using CellProfiler CP_object_tracking_example Jun 1, 2025 1 ❌ ❌ ❌
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Segmentation_Values_Testing Jun 1, 2025 1 ✅ ✅ ✅
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 2025_2D_spot_detection Jun 1, 2025 1 ✅ ✅ ✅
Tracking of mitochondria and capturing mitoflashes Capturing mitoflashes Jun 1, 2025 1 ✅ ✅ ❌
Using BioImage.IO models for image analysis in Galaxy Image prediction with BioImage.IO model (imported from uploaded file) Jun 1, 2025 3 ✅ ✅ ✅
Voronoi segmentation Voronoi segmentation Jun 1, 2025 1 ✅ ✅ ✅

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

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