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update interactive tools #610

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update interactive tools
nagoue Feb 20, 2026
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Merge branch 'main' into imaging_lab_update
nagoue Jun 26, 2026
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130 changes: 56 additions & 74 deletions communities/imaging/lab/sections/2_tools.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,77 +82,59 @@ tabs:
operation <br> *based on usage statistics from Galaxy’s main servers over the
last five years'
content:
- title_md: morphological_operations
description_md: |-
Apply morphological operations to images
(Tool usage: 298)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=morphological_operations">morphological_operations</a></li>
</ul>
- title_md: qupath_roi_splitter
description_md: |-
Split ROI coordinates of QuPath TMA annotation by cell type
(Tool usage: 232)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=qupath_roi_splitter">qupath_roi_splitter</a></li>
</ul>
- title_md: spyboat
description_md: |-
Wavelet analysis for 3d-image stacks
(Tool usage: 174)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=spyboat">spyboat</a></li>
</ul>
- title_md: yolo
description_md: |-
tools for building yolo workflows.
(Tool usage: 166)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=coco2labelme">coco2labelme</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>
</ul>
- title_md: orientationpy
description_md: |-
Compute image orientation
(Tool usage: 105)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=orientationpy">orientationpy</a></li>
</ul>
- title_md: wsi_extract_top_view
description_md: |-
WSI Extract Top View
(Tool usage: 58)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=ip_wsi_extract_top_view">ip_wsi_extract_top_view</a></li>
</ul>
- title_md: visceral_evaluatesegmentation
description_md: |-
Visceral Project - Evaluate Segmentation Tool
(Tool usage: 35)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=ip_visceral_evaluatesegmentation">ip_visceral_evaluatesegmentation</a></li>
</ul>
- title_md: vpt
description_md: |-
Vizgen Post-processing Tool
(Tool usage: 29)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=vpt_extract">vpt_extract</a></li>
<li><a href="{{ galaxy_base_url }}/?tool_id=vpt_segment">vpt_segment</a></li>
</ul>
- title_md: pdfimages
description_md: |-
PDF image extractor.
(Tool usage: 15)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=pdfimages">pdfimages</a></li>
</ul>
- title_md: omero_clean_rois_tables
description_md: |-
Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down
(Tool usage: 0)
<ul>
<li><a href="{{ galaxy_base_url }}/?tool_id=omero_clean_rois_tables">omero_clean_rois_tables</a></li>
</ul>
- title_md: interactivetool_anylabeling
description_md: >
Annotation tool that integrates an AI engine for fast and automatic labeling
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_anylabeling"
- title_md: interactive_tool_bellavista
description_md: >
Interactive data exploration
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_bellavista"
- title_md: interactive_tool_cellpose
description_md: >
Tool for cell and nucleus segmentation
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_cellpose"
- title_md: interactive_tool_cellprofiler
description_md: >
Image analysis software for identifying and quantifying cell phenotypes
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_cellprofiler"
- title_md: interactive_tool_cellxgene
description_md: >
Tool to deploy browser for visualization of single cell RNAseq data
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_cellxgene"
- title_md: interactive_tool_ilastik
description_md: >
Interactive machine learning and segmentation toolkit
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_ilastik"
- title_md: interactive_tool_napari
description_md: >
Interactive data exploration
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_napari"
- title_md: interactive_tool_qupath
description_md: >
Interactive tool for quantification of electrophoresis gel bands
inputs:
- datatypes:
- data
button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_qupath"