Suite ID	Tool IDs	Description	Suite first commit date	Homepage	Suite version	Suite conda package	Latest suite conda package version	Suite version status	ToolShed categories	EDAM operations	EDAM reduced operations	EDAM topics	EDAM reduced topics	Suite owner	Suite source	Suite parsed folder	bio.tool ID	bio.tool name	bio.tool description	biii ID	Number of tools on UseGalaxy.org (Main)	Number of tools on UseGalaxy.org.au	Number of tools on UseGalaxy.eu	Number of tools on UseGalaxy.fr	Number of tools on Galaxy@AuBi	Number of tools on UseGalaxy.be	Number of tools on UseGalaxy.cz	Number of tools on UseGalaxy.no	Suite users (last 5 years) (usegalaxy.eu)	Suite users (usegalaxy.eu)	Suite runs (last 5 years) (usegalaxy.eu)	Suite runs (usegalaxy.eu)	Suite users (last 5 years) (usegalaxy.org)	Suite users (usegalaxy.org)	Suite runs (last 5 years) (usegalaxy.org)	Suite runs (usegalaxy.org)	Suite users (last 5 years) (usegalaxy.org.au)	Suite users (usegalaxy.org.au)	Suite runs (last 5 years) (usegalaxy.org.au)	Suite runs (usegalaxy.org.au)	Suite runs on main servers	Suite runs (last 5 years) on main servers	Suite users on main servers	Suite users (last 5 years) on main servers	Related Workflows	Related Tutorials	To keep	Deprecated
mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	2019-01-08	https://github.com/bmcv	0.3-2	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	0	1	1	1	3	1	25	0	0	0	0	0	0	0	0	25	1	3	1			True	False
morphological_operations	morphological_operations	Apply morphological operations to images	2024-03-08	https://github.com/bmcv	1.12.0	scipy		To update	Imaging					imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations				scipy	0	0	1	0	0	0	0	0	1	1	298	298	0	0	0	0	0	0	0	0	298	298	1	1			True	False
omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down	2023-06-23		20230623	fiji	20250206	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id	2023-12-22		0.2.0	omero-py	5.11.1	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
omero_get_full_images	omero_get_full_images	Get full images from omero	2024-05-21		20240521	fiji	20250206	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels	2023-03-24		20230809	fiji	20250206	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements	2023-03-24		20240214	fiji	20250206	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
omero_upload	omero_dataset_to_plate, omero_filter, omero_get_id, omero_get_value, omero_import, omero_metadata_import, omero_roi_import	Interact with an OMERO.server using omero-py and ezomero.	2024-02-07	https://github.com/ome/omero-py/	5.18.0			To update	Imaging	Image analysis	Image analysis	Imaging, Data visualisation	Imaging, Data visualisation	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	omero	OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.		0	0	3	0	5	0	0	0	2	2	4	4	0	0	0	0	0	0	0	0	4	4	2	2	https://workflowhub.eu/workflows/1258?version=1, https://workflowhub.eu/workflows/1259?version=1	imaging/omero-suite	True	False
orientationpy	orientationpy	Compute image orientation	2024-03-12	https://github.com/bmcv	0.2.0.4	orientationpy	0.2.0.4	Up-to-date	Imaging					imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy				orientationj	0	0	1	0	0	0	0	0	2	2	105	105	0	0	0	0	0	0	0	0	105	105	2	2			True	False
overlay_images	ip_overlay_images	Overlay two images	2022-02-26	https://github.com/BMCV/galaxy-image-analysis	0.0.5	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		1	1	1	1	1	1	1	0	56	56	466	466	4	4	19	19	2	2	303	303	788	788	62	62	https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2	imaging/2D-spot-detection, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation	True	False
pdfimages	pdfimages	PDF image extractor.	2025-07-31	https://gitlab.freedesktop.org/poppler/poppler/	25.07.0	poppler		To update	Imaging, Natural Language Processing					iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages					0	0	1	0	0	0	0	0	2	2	15	15	0	0	0	0	0	0	0	0	15	15	2	2	https://usegalaxy.eu/published/workflow?id=cd5bae8c9bed36e2		True
permutate_axis	ip_permutate_axis	Permutates axes	2017-10-30	https://github.com/bmcv	0.2-2	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	0	1	1	0	2	0	42	0	0	0	0	0	0	0	0	42	0	2	0			True	False
plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	2024-06-19	https://github.com/bmcv	1.8.1	plant-seg		To update	Imaging	Network analysis, Quantification, Microscope image visualisation	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	plantseg	PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.		0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
points2labelimage	ip_points_to_label	Points to label image	2017-10-30	https://github.com/bmcv	0.5.0	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	1	1	1	2	3	46	77	0	0	0	0	0	0	0	0	77	46	3	2	https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=7a9621594d7b7849, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1848?version=1	imaging/2D-spot-detection, imaging/electrophoresis-gel-bands-image-analysis	True	False
points_association_nn	ip_points_association_nn	Association of points in consecutive frames	2021-07-22	https://github.com/BMCV/galaxy-image-analysis	0.0.3-2	numpy		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		1	0	1	0	0	1	1	0	6	6	47	47	0	0	0	0	0	0	0	0	47	47	6	6	https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1	imaging/detection-of-mitoflashes	True	False
projective_transformation	ip_projective_transformation	Projective transformation	2018-12-07	https://github.com/bmcv	0.1.2	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	0	1	1	3	6	21	86	0	0	0	0	0	0	0	0	86	21	6	3	https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890		True	False
projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	2018-12-07	https://github.com/bmcv	0.1.1	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	0	1	1	15	20	19258	21493	0	0	0	0	0	0	0	0	21493	19258	20	15	https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc		True	False
qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type	2023-04-12	https://github.com/npinter/ROIsplitter	0.3.2	geojson		To update	Imaging					galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter					0	0	1	0	0	0	1	0	11	11	232	232	0	0	0	0	0	0	0	0	232	232	11	11			True	False
repeat_channels	repeat_channels	Convert single-channel to multi-channel image	2024-04-25	https://github.com/bmcv	1.26.4	numpy		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	1	0	0	15	15	101	101	0	0	0	0	0	0	0	0	101	101	15	15	https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1	imaging/voronoi-segmentation	True	False
rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	2023-11-12	https://sites.google.com/site/costaspanagiotakis/research/cs	2023.11.12			To update	Imaging	Image analysis	Image analysis	Cell biology, Biomedical science, Imaging	Cell biology, Biomedical science, Imaging	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	rfove	RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.		0	0	1	0	0	0	0	0	7	7	15	15	0	0	0	0	0	0	0	0	15	15	7	7			True	False
ridge_filter	ridge_filter_skimage	Ridge filter for images	2025-12-08	https://scikit-image.org/docs/0.25.x/auto_examples/edges/plot_ridge_filter.html	0.22.0	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	scikit-image	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True
scale_image	ip_scale_image	Scales an image by re-sampling the image data.	2018-12-07	https://scikit-image.org/docs/0.25.x/auto_examples/transform/plot_rescale.html	0.25.2	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	scikit-image	0	0	1	0	0	0	1	1	17	20	751	870	0	0	0	0	0	0	0	0	870	751	20	17	https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc		True	False
segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	2022-10-07	https://github.com/bmcv	1.4	segmetrics	1.5	To update	Imaging	Image analysis	Image analysis			imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	segmetrics	0	0	1	0	0	1	1	0	3	3	88	88	0	0	0	0	0	0	0	0	88	88	3	3	https://workflowhub.eu/workflows/1517?version=1	imaging/parameter-tuning	True	False
slice_image	ip_slice_image	Slice image	2017-10-30	https://github.com/bmcv	0.3-4	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		1	1	1	0	0	0	1	1	3	6	4	104	0	0	0	0	1	1	48	48	152	52	7	4			True	False
split_image	ip_split_image	Split image along axes	2025-03-07	https://github.com/bmcv	2.3.5	numpy		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	1	0	0	17	17	232	232	0	0	0	0	0	0	0	0	232	232	17	17	https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1848?version=1	imaging/electrophoresis-gel-bands-image-analysis, imaging/process-image-bioimageio	True
split_labelmap	ip_split_labelmap	Split Labelmaps	2018-12-11	https://github.com/bmcv	0.2-3	scikit-image		To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		0	0	1	0	0	0	1	1	2	4	113	155	0	0	0	0	0	0	0	0	155	113	4	2			True	False
spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	2021-07-20	https://github.com/BMCV/galaxy-image-analysis	0.1	giatools	0.7.3	To update	Imaging	Image analysis	Image analysis	Imaging, Bioinformatics	Imaging, Bioinformatics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	galaxy_image_analysis	Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.		1	0	1	0	0	1	1	0	7	7	93	93	0	0	0	0	0	0	0	0	93	93	7	7	https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1, https://workflowhub.eu/workflows/1528?version=1	imaging/2D-spot-detection, imaging/detection-of-mitoflashes	True	False
spyboat	spyboat	Wavelet analysis for 3d-image stacks	2020-11-28	http://github.com/tensionhead/spyboat	0.1.2	spyboat		To update	Imaging, Graphics					iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat					0	0	1	0	0	1	1	0	6	6	174	174	0	0	0	0	0	0	0	0	174	174	6	6			True	False
superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	2023-06-20	https://superdsm.readthedocs.io	0.2.0	superdsm	0.4.0	To update	Imaging	Image analysis	Image analysis			imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	superdsm	0	0	1	0	0	0	1	0	5	5	26	26	0	0	0	0	0	0	0	0	26	26	5	5			True	False
upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server	2022-01-18		0.0.5	omero-py	5.11.1	To update	Imaging					lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0			True	False
visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool	2024-09-30	https://github.com/bmcv	0.5-2	visceral-evaluatesegmentation	2021.03.25	To update	Imaging					imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation				evaluatesegmentation-tool	0	0	1	0	0	0	1	1	1	2	10	35	0	0	0	0	0	0	0	0	35	10	2	1			True	False
voronoi_tesselation	voronoi_tessellation	Compute Voronoi tesselation	2024-03-09	https://github.com/bmcv	0.22.0	scikit-image		To update	Imaging	Image analysis, Image annotation, Visualisation, Data handling	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	Imaging, Software engineering, Literature and language	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	scikit-image	0	0	1	0	0	1	0	0	15	15	148	148	0	0	0	0	0	0	0	0	148	148	15	15	https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1	imaging/voronoi-segmentation	True	False
vpt	vpt_extract, vpt_segment	Vizgen Post-processing Tool	2025-04-29	https://vizgen.github.io/vizgen-postprocessing/	1.3.0			To update	Single Cell, Spatial Omics, Transcriptomics, Imaging					bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/vpt	https://github.com/bgruening/galaxytools/tree/master/tools/vpt					0	0	2	0	0	0	0	0	3	3	29	29	0	0	0	0	0	0	0	0	29	29	3	3			True
wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View	2017-10-30	https://github.com/bmcv	0.2-2	scikit-image		To update	Imaging					imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view					0	0	1	0	0	0	1	1	1	4	20	58	0	0	0	0	0	0	0	0	58	20	4	1			True	False
yolo	json2yolosegment, yolo_predict, yolo_training	tools for building yolo workflows.	2025-06-12	https://github.com/bgruening/galaxytools	8.3.0			To update	Imaging					bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo					0	0	3	0	0	2	0	0	6	6	166	166	0	0	0	0	0	0	0	0	166	166	6	6	https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://workflowhub.eu/workflows/1840?version=1	imaging/yolo-segmentation-training	True