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 logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoLeonid Kostrykin avatar Leonid Kostrykin

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 help Pre-requisites help 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 21, 2025 6
Analyse HeLa fluorescence siRNA screen feature_extraction Jun 21, 2025 6
End-to-End Tissue Microarray Image Analysis with Galaxy-ME GTN_Exemplar_002_TMA_workflow_Feb2025 Jun 21, 2025 1
Introduction to Image Analysis using Galaxy Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy' Jun 21, 2025 6
Nucleoli segmentation and feature extraction using CellProfiler CP_pipeline_IDR_training Jun 21, 2025 3
Object tracking using CellProfiler CP_object_tracking_example Jun 21, 2025 1
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Segmentation_Values_Testing Jun 21, 2025 1
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 2025_2D_spot_detection Jun 21, 2025 1
Tracking of mitochondria and capturing mitoflashes Capturing mitoflashes Jun 21, 2025 1
Using BioImage.IO models for image analysis in Galaxy Image prediction with BioImage.IO model (imported from uploaded file) Jun 21, 2025 3
Voronoi segmentation Voronoi segmentation Jun 21, 2025 1

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

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