imaging community automatic resources update

communities/imaging/lab/sections/2_tools.yml

@@ -109,6 +109,8 @@ tabs:
        (Tool usage: 166)
       <ul>
         <li><a href="{{ galaxy_base_url }}/?tool_id=coco2labelme">coco2labelme</a></li>
+        <li><a href="{{ galaxy_base_url }}/?tool_id=coco_annotation_visualizer">coco_annotation_visualizer</a></li>
+        <li><a href="{{ galaxy_base_url }}/?tool_id=edit_coco_annotation">edit_coco_annotation</a></li>
         <li><a href="{{ galaxy_base_url }}/?tool_id=json2yolosegment">json2yolosegment</a></li>
         <li><a href="{{ galaxy_base_url }}/?tool_id=yolo_predict">yolo_predict</a></li>
         <li><a href="{{ galaxy_base_url }}/?tool_id=yolo_training">yolo_training</a></li>

communities/imaging/lab/sections/3_workflows.yml

@@ -47,14 +47,14 @@ tabs:
     button_icon: view
   - title_md: Voronoi segmentation for Astronomy on Legacy Survey data
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysison topics related to Physics
+      analysis,Image annotation,Data handlingon topics related to Physics
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1730'
     button_tip: View workflow
     button_icon: view
   - title_md: OMERO Nuclei Cell Counting, Image Import, Annotation and Region of
       Interests (ROIs) Workflow
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysison topics related to 
+      analysis,Image annotation,Data handlingon topics related to 
       Bioimaging,Imaging
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1259'
     button_tip: View workflow
@@ -90,14 +90,19 @@ tabs:
     button_icon: tutorial
     button_link: 
       https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html
+  - title_md: Test tuto yolo DeepSeaSpy
+    description_md: ''
+    button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2170'
+    button_tip: View workflow
+    button_icon: view
   - title_md: 2024_OMERO_Basic_Upload
     description_md: Workflow covering operations related to Image analysis
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2108'
     button_tip: View workflow
     button_icon: view
   - title_md: Segmentation of Anatomical Structures in Medical Images
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2107'
     button_tip: View workflow
     button_icon: view
@@ -113,13 +118,13 @@ tabs:
     button_icon: view
   - title_md: Electrophoresis-Gel-Bands-Image-Analysis
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1848'
     button_tip: View workflow
     button_icon: view
   - title_md: YOLO training and segmentation workflow
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1840'
     button_tip: View workflow
     button_icon: view
@@ -131,13 +136,13 @@ tabs:
   - title_md: Workflow constructed from Tutorial 'Introduction to Image Analysis
       using Galaxy'
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1532'
     button_tip: View workflow
     button_icon: view
   - title_md: 2025_2D_spot_detection
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1528'
     button_tip: View workflow
     button_icon: view
@@ -149,13 +154,13 @@ tabs:
     button_icon: view
   - title_md: Voronoi segmentation
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1522'
     button_tip: View workflow
     button_icon: view
   - title_md: Segmentation_Values_Testing
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1517'
     button_tip: View workflow
     button_icon: view
@@ -171,7 +176,7 @@ tabs:
     button_icon: view
   - title_md: feature_extraction
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1508'
     button_tip: View workflow
     button_icon: view
@@ -195,9 +200,26 @@ tabs:
     button_icon: tutorial
     button_link: 
       https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html
+  - title_md: '3Dtrees: Point cloud processing'
+    description_md: ''
+    button_link: https://usegalaxy.eu/published/workflow?id=732d9b238123a3c5
+    button_tip: View workflow
+    button_icon: view
+  - title_md: Cell segmentation and counting
+    description_md: Workflow covering operations related to Visualisation,Image 
+      analysis,Image annotation,Data handling
+    button_link: https://usegalaxy.eu/published/workflow?id=80baa108e6951b07
+    button_tip: View workflow
+    button_icon: view
+  - title_md: Voronoi segmentation
+    description_md: Workflow covering operations related to Visualisation,Image 
+      analysis,Image annotation,Data handling
+    button_link: https://usegalaxy.eu/published/workflow?id=adc8fba66982aeef
+    button_tip: View workflow
+    button_icon: view
   - title_md: YOLO training and segmentation workflow
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0
     button_tip: View workflow
     button_icon: view
@@ -208,19 +230,19 @@ tabs:
     button_icon: view
   - title_md: Voronoi segmentation for Astronomy on Legacy Survey data
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d
     button_tip: View workflow
     button_icon: view
   - title_md: Voronoi segmentation
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2
     button_tip: View workflow
     button_icon: view
   - title_md: 2025_Generic_Nuclei_Segmentation
     description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+      analysis,Image annotation,Data handling
     button_link: https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac
     button_tip: View workflow
     button_icon: view

communities/imaging/lab/sections/4_tutorials.yml

@@ -3,7 +3,8 @@ title: Community curated tutorials
 tabs:
 - id: imaging
   title: Imaging
-  heading_md: 'Top 10 most visited tutorials for the Topic : Imaging'
+  heading_md: 'Top 10 most visited tutorials for the Topic : Imaging. <br/> Visitors
+    : Number of unique visitors automatically calculated using Plausible.'
   content:
   - title_md: "Nucleoli segmentation and feature extraction using CellProfiler\n (Visitors:
       3426157)"

communities/imaging/lab/tools/all/APOSTL.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/CIRM-CFBP.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/ChemFlow.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Coloc-stats.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/GASLINI.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Galaxy@AuBi.yaml

@@ -125,6 +125,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Galaxy@Pasteur.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/GalaxyTrakr.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/IPK_Galaxy_Blast_Suite.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/ImmPort_Galaxy.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/InteractoMIX.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Lebanese_University_Galaxy.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Local_Galaxy.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/MBAC_Metabiome_Portal.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/MISSISSIPPI.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''

communities/imaging/lab/tools/all/Mandoiu_Lab.yaml

@@ -128,6 +128,12 @@ tools:
 - name: coco2labelme
   owner: bgruening
   tool_panel_section_id: ''
+- name: coco_annotation_visualizer
+  owner: bgruening
+  tool_panel_section_id: ''
+- name: edit_coco_annotation
+  owner: bgruening
+  tool_panel_section_id: ''
 - name: json2yolosegment
   owner: bgruening
   tool_panel_section_id: ''