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imaging community resources update
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‎communities/imaging/lab/sections/2_tools.yml‎

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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=qupath_roi_splitter">qupath_roi_splitter</a></li>
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</ul>
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- title_md: spyboat
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description_md: |-
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Wavelet analysis for 3d-image stacks
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(Tool usage: 174)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=spyboat">spyboat</a></li>
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</ul>
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- title_md: yolo
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description_md: |-
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tools for building yolo workflows.
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(Tool usage: 166)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=coco2labelme">coco2labelme</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=coco_annotation_visualizer">coco_annotation_visualizer</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=edit_coco_annotation">edit_coco_annotation</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=json2yolosegment">json2yolosegment</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=yolo_predict">yolo_predict</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=yolo_training">yolo_training</a></li>
@@ -142,17 +137,24 @@ tabs:
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<li><a href="{{ galaxy_base_url }}/?tool_id=vpt_extract">vpt_extract</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=vpt_segment">vpt_segment</a></li>
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</ul>
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- title_md: pdfimages
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description_md: |-
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PDF image extractor.
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(Tool usage: 15)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=pdfimages">pdfimages</a></li>
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</ul>
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- title_md: omero_clean_rois_tables
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description_md: |-
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Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=omero_clean_rois_tables">omero_clean_rois_tables</a></li>
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</ul>
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- title_md: omero_get_children_ids
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description_md: |-
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Get omero id of children of an omero object id
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=omero_get_children_ids">omero_get_children_ids</a></li>
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</ul>
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- title_md: omero_get_full_images
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description_md: |-
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Get full images from omero
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=omero_get_full_images">omero_get_full_images</a></li>
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</ul>

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

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button_icon: view
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- title_md: Nucleoli segmentation using CellProfiler (EOSC-Life D6)
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description_md: Workflow covering operations related to
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Quantification,Parsing,Image analysison topics related to
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Parsing,Quantification,Image analysison topics related to
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Bioimaging,Imaging
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=41'
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button_tip: View workflow
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button_icon: view
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- title_md: Object tracking using CellProfiler
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description_md: Workflow covering operations related to
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Quantification,Parsing,Image analysison topics related to
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Parsing,Quantification,Image analysison topics related to
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Bioimaging,Imaging
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=115'
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button_tip: View workflow
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button_icon: tutorial
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button_link:
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https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html
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- title_md: Test tuto yolo DeepSeaSpy
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description_md: ''
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2170'
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button_tip: View workflow
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button_icon: view
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- title_md: 2024_OMERO_Basic_Upload
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description_md: Workflow covering operations related to Image analysis
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2108'
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button_icon: view
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- title_md: YOLO training and segmentation workflow
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description_md: Workflow covering operations related to Visualisation,Image
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annotation,Data handling,Image analysis
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annotation,Image analysis,Data handling
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1840'
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button_tip: View workflow
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button_icon: view
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button_icon: view
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- title_md: CP_pipeline_IDR_training
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description_md: Workflow covering operations related to
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Quantification,Parsing,Image analysis
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Parsing,Quantification,Image analysis
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1505'
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button_tip: View workflow
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button_icon: view
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- title_md: CP_object_tracking_example
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description_md: Workflow covering operations related to
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Quantification,Parsing,Image analysis
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Parsing,Quantification,Image analysis
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button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1503'
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button_tip: View workflow
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button_icon: view
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button_icon: tutorial
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button_link:
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https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html
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- title_md: YOLO training and segmentation workflow
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- title_md: '3Dtrees: Point cloud processing'
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description_md: ''
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button_link: https://usegalaxy.eu/published/workflow?id=732d9b238123a3c5
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button_tip: View workflow
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button_icon: view
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- title_md: Cell segmentation and counting
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description_md: Workflow covering operations related to Visualisation,Image
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annotation,Data handling,Image analysis
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button_link: https://usegalaxy.eu/published/workflow?id=80baa108e6951b07
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button_tip: View workflow
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button_icon: view
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- title_md: Voronoi segmentation
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description_md: Workflow covering operations related to Visualisation,Image
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annotation,Data handling,Image analysis
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button_link: https://usegalaxy.eu/published/workflow?id=adc8fba66982aeef
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button_tip: View workflow
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button_icon: view
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- title_md: YOLO training and segmentation workflow
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description_md: Workflow covering operations related to Visualisation,Image
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annotation,Image analysis,Data handling
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button_link: https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0
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button_tip: View workflow
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button_icon: view

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

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- name: ip_overlay_images
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owner: imgteam
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tool_panel_section_id: ''
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- name: pdfimages
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_permutate_axis
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owner: imgteam
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tool_panel_section_id: ''
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- name: ip_spot_detection_2d
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owner: imgteam
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tool_panel_section_id: ''
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- name: spyboat
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_superdsm
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owner: imgteam
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tool_panel_section_id: ''
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- name: coco2labelme
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owner: bgruening
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tool_panel_section_id: ''
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- name: coco_annotation_visualizer
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owner: bgruening
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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tool_panel_section_id: ''
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- name: json2yolosegment
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owner: bgruening
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tool_panel_section_id: ''

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

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- name: ip_overlay_images
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owner: imgteam
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tool_panel_section_id: ''
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- name: pdfimages
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_permutate_axis
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owner: imgteam
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tool_panel_section_id: ''
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- name: ip_spot_detection_2d
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owner: imgteam
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tool_panel_section_id: ''
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- name: spyboat
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_superdsm
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owner: imgteam
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tool_panel_section_id: ''
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- name: coco2labelme
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owner: bgruening
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tool_panel_section_id: ''
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- name: coco_annotation_visualizer
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owner: bgruening
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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tool_panel_section_id: ''
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- name: json2yolosegment
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owner: bgruening
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tool_panel_section_id: ''

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

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- name: ip_overlay_images
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owner: imgteam
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tool_panel_section_id: ''
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- name: pdfimages
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_permutate_axis
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owner: imgteam
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tool_panel_section_id: ''
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- name: ip_spot_detection_2d
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owner: imgteam
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tool_panel_section_id: ''
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- name: spyboat
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_superdsm
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owner: imgteam
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tool_panel_section_id: ''
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- name: coco2labelme
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owner: bgruening
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tool_panel_section_id: ''
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- name: coco_annotation_visualizer
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owner: bgruening
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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tool_panel_section_id: ''
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- name: json2yolosegment
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owner: bgruening
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tool_panel_section_id: ''

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

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- name: ip_overlay_images
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owner: imgteam
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tool_panel_section_id: ''
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- name: pdfimages
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_permutate_axis
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owner: imgteam
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tool_panel_section_id: ''
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- name: ip_spot_detection_2d
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owner: imgteam
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tool_panel_section_id: ''
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- name: spyboat
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owner: iuc
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tool_panel_section_id: ''
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- name: ip_superdsm
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owner: imgteam
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tool_panel_section_id: ''
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- name: coco2labelme
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owner: bgruening
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tool_panel_section_id: ''
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- name: coco_annotation_visualizer
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owner: bgruening
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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tool_panel_section_id: ''
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- name: json2yolosegment
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owner: bgruening
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tool_panel_section_id: ''

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

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- name: orientationpy
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owner: imgteam
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tool_panel_section_id: ''
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- name: pdfimages
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owner: iuc
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- name: ip_permutate_axis
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- name: ip_spot_detection_2d
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tool_panel_section_id: ''
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- name: ip_superdsm
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- name: coco2labelme
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owner: bgruening
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- name: coco_annotation_visualizer
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owner: bgruening
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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tool_panel_section_id: ''
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- name: json2yolosegment
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tool_panel_section_id: ''

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

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- name: ip_overlay_images
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owner: imgteam
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- name: pdfimages
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- name: ip_permutate_axis
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- name: ip_spot_detection_2d
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- name: coco2labelme
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owner: bgruening
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- name: coco_annotation_visualizer
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tool_panel_section_id: ''
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- name: edit_coco_annotation
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owner: bgruening
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- name: json2yolosegment
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tool_panel_section_id: ''

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

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- name: ip_overlay_images
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owner: imgteam
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- name: pdfimages
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owner: iuc
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- name: ip_permutate_axis
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- name: coco_annotation_visualizer
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- name: edit_coco_annotation
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- name: json2yolosegment
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‎communities/imaging/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml‎

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- name: ip_overlay_images
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- name: json2yolosegment
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