Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on GalaxyTrakr	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	1	1	39	6541
2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	1	1	19	13760
2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	1	1	18	6834
2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	1	1	39	656
2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	1	1	35	6156
3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0
anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	1	1	0	40
background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0
bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	1	1	38	1523
bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	2
binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	1	1	34	1273
binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	29
bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	9
bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0
cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0
cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	23	19	178	4614
cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	1	1	0	8	43
color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	1	16
colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0
concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	3	78
coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	8	16546
count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	1	1	25	272
curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	0	1	12
detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	2	46
graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	2	2	43	2605
hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	1	1	41	621
image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0
image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	0	2	12
imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	7	21825
imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20170530			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	27	27	26	1537
incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0
labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	36
landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	1	1	9	857
mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	1	1	0	37
measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	25
morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	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	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0
omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0
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								To update		Imaging	omero_clean_rois_tables	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	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	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	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0
omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	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	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	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	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	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	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0
orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0
overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	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	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	1	0	21	60
permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	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	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	42
plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	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.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0
points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	2	41
points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	31
points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	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	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	0	2	29
projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	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	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	1	85
projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	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	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	9	21343
qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	1	0	5	59
repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	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	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0
rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	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.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	7
scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	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	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	1	1	9	512
segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	1	0	2	3
slice_image	ip_slice_image	Slice image	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	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	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	1	1	0	102
split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	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	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	1	0	42
spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	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.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	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	0.0.3-2	imageio		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	1	0	3	16
spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	1	0	1	67
superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	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.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	1	0	2	16
upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	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	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0
visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	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	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	1	1	0	25
voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	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	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0
woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0
wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	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	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	1	1	0	38