imaging community resources update

Author: scorreard

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

@@ -46,15 +46,15 @@ tabs:
     button_tip: View workflow
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotationon 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 
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotationon 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
@@ -66,16 +66,14 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: Nucleoli segmentation using CellProfiler (EOSC-Life D6)
-    description_md: Workflow covering operations related to 
-      Quantification,Parsing,Image analysison topics related to 
-      Bioimaging,Imaging
+    description_md: Workflow covering operations related to Quantification,Image
+      analysis,Parsingon topics related to Bioimaging,Imaging
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=41'
     button_tip: View workflow
     button_icon: view
   - title_md: Object tracking using CellProfiler
-    description_md: Workflow covering operations related to 
-      Quantification,Parsing,Image analysison topics related to 
-      Bioimaging,Imaging
+    description_md: Workflow covering operations related to Quantification,Image
+      analysis,Parsingon topics related to Bioimaging,Imaging
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=115'
     button_tip: View workflow
     button_icon: view
@@ -90,14 +88,19 @@ 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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
@@ -112,14 +115,14 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: Electrophoresis-Gel-Bands-Image-Analysis
-    description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
+    description_md: Workflow covering operations related to Image analysis,Data 
+      handling,Visualisation,Image annotation
     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
@@ -130,14 +133,14 @@ tabs:
     button_icon: view
   - 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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
@@ -148,14 +151,14 @@ tabs:
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
@@ -170,20 +173,20 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: feature_extraction
-    description_md: Workflow covering operations related to Visualisation,Image 
-      annotation,Data handling,Image analysis
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
   - title_md: CP_pipeline_IDR_training
-    description_md: Workflow covering operations related to 
-      Quantification,Parsing,Image analysis
+    description_md: Workflow covering operations related to Quantification,Image
+      analysis,Parsing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1505'
     button_tip: View workflow
     button_icon: view
   - title_md: CP_object_tracking_example
-    description_md: Workflow covering operations related to 
-      Quantification,Parsing,Image analysis
+    description_md: Workflow covering operations related to Quantification,Image
+      analysis,Parsing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1503'
     button_tip: View workflow
     button_icon: view
@@ -195,9 +198,26 @@ 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 Data handling,Image 
+      analysis,Visualisation,Image annotation
+    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 Data handling,Image 
+      analysis,Visualisation,Image annotation
+    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
+    description_md: Workflow covering operations related to Image analysis,Data 
+      handling,Visualisation,Image annotation
     button_link: https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0
     button_tip: View workflow
     button_icon: view
@@ -207,20 +227,20 @@ tabs:
     button_tip: View workflow
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     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
+    description_md: Workflow covering operations related to Data handling,Image 
+      analysis,Visualisation,Image annotation
     button_link: https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac
     button_tip: View workflow
     button_icon: view

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: ''