Merge pull request #6523 from beatrizserrano/add-subtopics-to-imaging

kostrykin · web-flow · commit af239db8d61e · 2025-11-26T16:39:35.000+01:00
Add subtopics to imaging
diff --git a/topics/fair/tutorials/bioimage-REMBI/tutorial.md b/topics/fair/tutorials/bioimage-REMBI/tutorial.md
@@ -2,6 +2,7 @@
 layout: tutorial_hands_on
 title: REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
 level: Introductory
+subtopic: introduction
 zenodo_link: ''
 
 questions:
diff --git a/topics/fair/tutorials/bioimage-metadata/tutorial.md b/topics/fair/tutorials/bioimage-metadata/tutorial.md
@@ -2,6 +2,7 @@
 layout: tutorial_hands_on
 title: FAIR Bioimage Metadata
 level: Introductory
+subtopic: introduction
 zenodo_link: ''
 
 questions:
diff --git a/topics/imaging/metadata.yaml b/topics/imaging/metadata.yaml
@@ -25,3 +25,23 @@ references:
     title: "Workflows for microscopy image analysis and cellular phenotyping"
     link: "https://www.sciencedirect.com/science/article/pii/S0168165617315444"
     summary: ""
+  -
+    authors: "Leonid Kostrykin et al"
+    title: "Enhancing the image analysis community in Galaxy."
+    link: "https://doi.org/10.37044/osf.io/w8dsz"
+    summary: ""
+  -
+    authors: "Leonid Kostrykin et al"
+    title: "Development of FAIR image analysis workflows and training in Galaxy"
+    link: "https://doi.org/10.37044/osf.io/hbw6m_v1"
+    summary: ""
+subtopics:
+- id: introduction
+  title: "Introduction"
+  description: "Start here if you are new to Image Analysis in Galaxy"
+- id: analyses
+  title: "Analyses"
+  description: "These tutorials will help you analyse your image data"
+- id: advanced
+  title: "Advanced topics"
+  description: "Tutorials covering advanced topics"
diff --git a/topics/imaging/tutorials/2D-spot-detection/tutorial.md b/topics/imaging/tutorials/2D-spot-detection/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines"
 level: Introductory
+subtopic: analyses
 questions:
   - "How do I analyze fluorescence markers in a 2D image?"
   - "How do I create labels from the detected bright spots?"
diff --git a/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.md b/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: Tracking of mitochondria and capturing mitoflashes
 level: Intermediate
+subtopic: analyses
 zenodo_link: https://zenodo.org/records/14071552
 questions:
 - What are mitoflashes, and why are they relevant for understanding mitochondrial function?
diff --git a/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.md b/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
 level: Intermediate
+subtopic: analyses
 questions:
 - How can specific bands on an electrophoresis gel image be selected using QuPath?
 - How is a region of interest (ROI) GeoJSON file prepared?
diff --git a/topics/imaging/tutorials/hela-screen-analysis/tutorial.md b/topics/imaging/tutorials/hela-screen-analysis/tutorial.md
@@ -4,6 +4,7 @@ layout: tutorial_hands_on
 title: "Analyse HeLa fluorescence siRNA screen"
 zenodo_link: https://zenodo.org/record/3362976
 level: Intermediate
+subtopic: analyses
 questions:
   - "How do I analyze a HeLa fluorescence siRNA screen?"
   - "How do I segment cell nuclei?"
diff --git a/topics/imaging/tutorials/imaging-introduction/tutorial.md b/topics/imaging/tutorials/imaging-introduction/tutorial.md
@@ -4,6 +4,7 @@ layout: tutorial_hands_on
 title: "Introduction to Image Analysis using Galaxy"
 zenodo_link: https://zenodo.org/record/3362976
 level: Introductory
+subtopic: introduction
 questions:
   - "How do I use Galaxy with imaging data?"
   - "How do I convert images using Galaxy?"
diff --git a/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md b/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: End-to-End Tissue Microarray Image Analysis with Galaxy-ME
 level: Intermediate
+subtopic: analyses
 zenodo_link: https://doi.org/10.5281/zenodo.7622545
 questions:
 - What tools are available for pre-processing multiplex tissue images in Galaxy?
diff --git a/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md b/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: Object tracking using CellProfiler
 level: Intermediate
+subtopic: analyses
 zenodo_link: https://doi.org/10.5281/zenodo.4567084
 requirements:
   -
diff --git a/topics/imaging/tutorials/omero-suite/tutorial.md b/topics/imaging/tutorials/omero-suite/tutorial.md
@@ -2,6 +2,7 @@
 layout: tutorial_hands_on
 title: Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
 level: Intermediate
+subtopic: introduction
 zenodo_link: https://zenodo.org/records/14205500
 questions:
 - How can I use Galaxy to upload images and metadata into OMERO?
diff --git a/topics/imaging/tutorials/parameter-tuning/tutorial.md b/topics/imaging/tutorials/parameter-tuning/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy"
 level: Introductory
+subtopic: advanced
 questions:
   - What are the challenges of using the same settings for every biological image, and how does parameter tuning address these challenges?
   - How can we choose the best filters for preprocessing images for nuclei segmentation?
diff --git a/topics/imaging/tutorials/process-image-bioimageio/tutorial.md b/topics/imaging/tutorials/process-image-bioimageio/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: Using BioImage.IO models for image analysis in Galaxy
 level: Intermediate
+subtopic: analyses
 zenodo_link: 'https://zenodo.org/record/6647674'
 questions:
 - How can I apply a pre-trained deep learning model to an image?
diff --git a/topics/imaging/tutorials/tutorial-CP/tutorial.md b/topics/imaging/tutorials/tutorial-CP/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: "Nucleoli segmentation and feature extraction using CellProfiler"
 level: Intermediate
+subtopic: analyses
 questions:
 - How do I run an image analysis pipeline on public data using CellProfiler?
 - How do I analyse the DNA channel of fluorescence siRNA screens?
diff --git a/topics/imaging/tutorials/voronoi-segmentation/tutorial.md b/topics/imaging/tutorials/voronoi-segmentation/tutorial.md
@@ -3,6 +3,7 @@ layout: tutorial_hands_on
 
 title: Voronoi segmentation
 level: Intermediate
+subtopic: analyses
 zenodo_link: https://zenodo.org/records/15172302
 questions:
   - How do I partition an image into regions based on which object they are nearest to (Voronoi segmentation)?
diff --git a/topics/imaging/tutorials/yolo-segmentation-training/tutorial.md b/topics/imaging/tutorials/yolo-segmentation-training/tutorial.md
@@ -2,6 +2,7 @@
 layout: tutorial_hands_on
 title: Training Custom YOLO Models for Segmentation of Bioimages
 level: Intermediate
+subtopic: advanced
 zenodo_link: https://zenodo.org/records/16096782
 questions:
 - Why use YOLO for segmentation in bioimage analysis?

Original file line number	Diff line number	Diff line change
`@@ -3,6 +3,7 @@ layout: tutorial_hands_on`
`3`	`3`
`4`	`4`	`title: Object tracking using CellProfiler`
`5`	`5`	`level: Intermediate`
	`6`	`+subtopic: analyses`
`6`	`7`	`zenodo_link: https://doi.org/10.5281/zenodo.4567084`
`7`	`8`	`requirements:`
`8`	`9`	`-`