Expand Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated
Galaxy Workflow - ARC2OMERO WorkflowHub 2116 https://workflowhub.eu/workflows/2116?version=1 Riccardo Massei arc, nfdi4bioimage, omero, rdm 2026-03-23 2026-03-23 1 1 15.0 param_value_from_file, Cut1, Grep1, tp_awk_tool, xlsx2tsv, datamash_transpose, unzip, omero_import, filter_tabular, omero_metadata_import, regexColumn1, jq Image analysis Biomedical science, Data curation and archival CC-BY-4.0 BioImage Informatics and Analysis Workflows, UFZ - Image Data Management and Processing Workflows True False
Wound Healing Scratch Assay Image Analysis WorkflowHub 782 https://workflowhub.eu/workflows/782?version=1 Christian Tischer bioimage, imagej 2024-03-06 2025-12-19 1 1 1.0 woundhealing_scratch_assay CC-BY-4.0 EMBL-Bioimage Analysis Support True False
YOLO training and segmentation WorkflowHub 1811 https://workflowhub.eu/workflows/1811?version=1 Yi Sun, Arif Khan bioimage, yolo 2025-07-16 2025-07-16 1 1 5.0 Bioimaging, Machine learning GPL-3.0-or-later EMBL-Bioimage Analysis Support, BioImage Informatics and Analysis Workflows True False
EOSC4Cancer D2.2 WorkflowHub 1381 https://workflowhub.eu/workflows/1381?version=2 Jeanne Chèneby, Hakim Achterberg, Dario Longo, Francesco Gammaraccio, Robin Navest eosc4cancer, galaxy, xnat, cbioportal, image processing, imaging 2025-10-21 2025-11-10 2 2 0.0 Imaging CC-BY-4.0 EOSC4Cancer True False
Voronoi segmentation for Astronomy on Legacy Survey data WorkflowHub 1730 https://workflowhub.eu/workflows/1730?version=1 Andrei Variu, Riccardo Massei, Even Moa  Myklebust segmentation, voronoi, astronomy, imageanaylsis 2025-06-13 2025-07-11 1 1 18.0 ip_filter_standard, ip_2d_feature_extraction, ip_split_image, ip_overlay_images, ip_convertimage, ip_binary_to_labelimage, voronoi_tessellation, astropy_fits2bitmap, __EXTRACT_DATASET__, image_math, ip_threshold, ip_histogram_equalization, colorize_labels, repeat_channels, desi_legacy_survey_astro_tool, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis Physics MIT 10.48546/workflowhub.workflow.1730.1 EuroScienceGateway True False
2024_OMERO_Basic_Upload WorkflowHub 2108 https://workflowhub.eu/workflows/2108?version=1 gtn, galaxy, nfdi4bioimage, omero, rdm, imageanaylsis 2026-03-09 2026-03-09 1 1 7.0 param_value_from_file, tp_replace_in_line, split_file_to_collection, omero_roi_import, omero_import, omero_metadata_import, Convert characters1 Image analysis CC-BY-4.0 Galaxy Training Network True False
Segmentation of Anatomical Structures in Medical Images WorkflowHub 2107 https://workflowhub.eu/workflows/2107?version=1 gtn, galaxy, imaging 2026-03-09 2026-03-09 1 1 26.0 compose_text_param, ridge_filter_skimage, add_line_to_file, ip_2d_feature_extraction, param_value_from_file, ip_binary_to_labelimage, tp_replace_in_line, ip_2d_filter_segmentation_by_features, clip_image, ip_scale_image, ip_threshold, Add_a_column1, ip_concat_channels, highdicom_dicom2tiff, query_tabular, tp_text_file_with_recurring_lines, Convert characters1 Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
ISCC - image analysis workflow example WorkflowHub 2089 https://workflowhub.eu/workflows/2089?version=1 gtn, galaxy, bioimaging, imaging 2026-02-16 2026-02-16 1 1 6.0 iscc_sum, param_value_from_file, ip_split_image, __EXTRACT_DATASET__, ip_threshold, iscc_sum_verify Image analysis Apache-2.0 Galaxy Training Network True False
BiaPy WorkflowHub 2088 https://workflowhub.eu/workflows/2088?version=1 gtn, galaxy, imaging 2026-02-16 2026-02-16 1 1 2.0 biapy, libcarna_render Image analysis CC-BY-4.0 Galaxy Training Network True False
Electrophoresis-Gel-Bands-Image-Analysis WorkflowHub 1848 https://workflowhub.eu/workflows/1848?version=1 electrophoresis_gel, gtn, galaxy, name:band_intensity, name:bioimaging, name:qupath, roi 2025-08-11 2025-08-11 1 1 6.0 ip_imageinfo, ip_2d_feature_extraction, ip_split_image, ip_points_to_label, graphicsmagick_image_convert, interactive_tool_qupath Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
YOLO training and segmentation workflow WorkflowHub 1840 https://workflowhub.eu/workflows/1840?version=1 bioimage, gtn, galaxy, yolo 2025-07-28 2025-08-04 1 1 5.0 graphicsmagick_image_convert, ip_histogram_equalization, yolo_training, interactive_tool_anylabeling, json2yolosegment Visualisation, Image annotation, Data handling, Image analysis GPL-3.0-or-later Galaxy Training Network True False
Ludwig - Image recognition model - MNIST WorkflowHub 1614 https://workflowhub.eu/workflows/1614?version=1 gtn, galaxy, imagerecognition, ludwig, mnist 2025-06-02 2025-06-02 1 1 1.0 ludwig_experiment AGPL-3.0-or-later Galaxy Training Network True False
Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy' WorkflowHub 1532 https://workflowhub.eu/workflows/1532?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 7.0 ip_filter_standard, ip_imageinfo, ip_overlay_images, ip_binary_to_labelimage, ip_threshold, ip_histogram_equalization, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
2025_2D_spot_detection WorkflowHub 1528 https://workflowhub.eu/workflows/1528?version=1 gtn, galaxy, idr, segmentation, smfish, bioimaging 2025-06-02 2025-06-02 1 1 6.0 ip_overlay_images, ip_points_to_label, unzip, idr_download_by_ids, ip_histogram_equalization, ip_spot_detection_2d Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
Image prediction with BioImage.IO model (imported from uploaded file) WorkflowHub 1526 https://workflowhub.eu/workflows/1526?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 8.0 ip_split_image, ip_overlay_images, ip_binary_to_labelimage, __EXTRACT_DATASET__, image_math, ip_threshold, bioimage_inference Image analysis CC-BY-4.0 Galaxy Training Network True False
Voronoi segmentation WorkflowHub 1522 https://workflowhub.eu/workflows/1522?version=1 gtn, galaxy, segmentation, voronoi, imageanaylsis 2025-06-02 2025-06-02 1 1 11.0 ip_filter_standard, ip_2d_feature_extraction, ip_overlay_images, voronoi_tessellation, ip_convertimage, ip_binary_to_labelimage, image_math, ip_threshold, colorize_labels, repeat_channels, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
Segmentation_Values_Testing WorkflowHub 1517 https://workflowhub.eu/workflows/1517?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 7.0 ip_filter_standard, ip_segmetrics, param_value_from_file, ip_threshold, ip_histogram_equalization, collapse_dataset, tp_split_on_column Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
GTN_Exemplar_002_TMA_workflow_Feb2025 WorkflowHub 1514 https://workflowhub.eu/workflows/1514?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 10.0 basic_illumination, mesmer, ip_convertimage, quantification, vitessce_spatial, scimap_phenotyping, unet_coreograph, scimap_mcmicro_to_anndata, ashlar, rename_tiff_channels MIT Galaxy Training Network True False
analyze_screen WorkflowHub 1512 https://workflowhub.eu/workflows/1512?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 2.0 , collapse_dataset MIT Galaxy Training Network True False
feature_extraction WorkflowHub 1508 https://workflowhub.eu/workflows/1508?version=1 gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 6.0 ip_filter_standard, ip_2d_feature_extraction, ip_binary_to_labelimage, ip_threshold, ip_2d_filter_segmentation_by_features Visualisation, Image annotation, Data handling, Image analysis MIT Galaxy Training Network True False
CP_pipeline_IDR_training WorkflowHub 1505 https://workflowhub.eu/workflows/1505?version=1 cellprofiler, gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 25.0 cp_measure_texture, cp_enhance_or_suppress_features, cp_common, cp_gray_to_color, cp_measure_granularity, cp_measure_object_size_shape, cp_save_images, cp_measure_object_intensity, cp_cellprofiler, cp_convert_objects_to_image, cp_image_math, idr_download_by_ids, cp_relate_objects, cp_display_data_on_image, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_export_to_spreadsheet, cp_mask_image, cp_identify_primary_objects Quantification, Parsing, Image analysis CC-BY-4.0 Galaxy Training Network True False
CP_object_tracking_example WorkflowHub 1503 https://workflowhub.eu/workflows/1503?version=1 cellprofiler, gtn, galaxy, imaging 2025-06-02 2025-06-02 1 1 12.0 cp_color_to_gray, cp_tile, cp_measure_object_size_shape, cp_overlay_outlines, cp_save_images, unzip, cp_measure_object_intensity, cp_cellprofiler, cp_export_to_spreadsheet, cp_common, cp_identify_primary_objects, cp_track_objects Quantification, Parsing, Image analysis CC-BY-4.0 Galaxy Training Network True False
Object tracking using CellProfiler WorkflowHub 115 https://workflowhub.eu/workflows/115?version=1 cellprofiler, galaxy, image processing, imaging 2021-03-21 2023-07-03 1 1 12.0 cp_color_to_gray, cp_tile, cp_measure_object_size_shape, cp_overlay_outlines, cp_save_images, unzip, cp_measure_object_intensity, cp_cellprofiler, cp_export_to_spreadsheet, cp_common, cp_identify_primary_objects, cp_track_objects Quantification, Parsing, Image analysis Bioimaging, Imaging Apache-2.0 IBISBA Workflows, Euro-BioImaging True False
Nucleoli segmentation using CellProfiler (EOSC-Life D6) WorkflowHub 41 https://workflowhub.eu/workflows/41?version=2 cellprofiler, galaxy, image processing, imaging 2020-11-03 2023-07-03 2 1 25.0 cp_measure_texture, cp_enhance_or_suppress_features, cp_common, cp_gray_to_color, cp_measure_granularity, cp_measure_object_size_shape, cp_save_images, cp_measure_object_intensity, cp_cellprofiler, cp_convert_objects_to_image, cp_image_math, idr_download_by_ids, cp_relate_objects, cp_display_data_on_image, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_export_to_spreadsheet, cp_mask_image, cp_identify_primary_objects Quantification, Parsing, Image analysis Bioimaging, Imaging Apache-2.0 IBISBA Workflows, Euro-BioImaging, EOSC-Life WP3 True False
OMERO Nuclei Cell Counting, Image Import, Annotation and Region of Interests (ROIs) Workflow WorkflowHub 1259 https://workflowhub.eu/workflows/1259?version=1 Riccardo Massei fair, fair workflows, omero, rdm, workflows, bioimaging, imaging 2025-01-28 2025-03-03 1 1 20.0 imagej2_analyze_particles_binary, ip_filter_standard, ip_2d_feature_extraction, tp_replace_in_column, ip_convertimage, ip_binary_to_labelimage, param_value_from_file, tp_awk_tool, split_file_to_collection, omero_roi_import, omero_filter, tp_find_and_replace, ip_threshold, omero_import, ip_histogram_equalization, omero_metadata_import, Convert characters1, collection_element_identifiers Visualisation, Image annotation, Data handling, Image analysis Bioimaging, Imaging MIT 10.48546/workflowhub.workflow.1259.1 UFZ - Image Data Management and Processing Workflows True False
OMERO Image Import, Annotation and Region of Interests (ROIs) Workflow WorkflowHub 1258 https://workflowhub.eu/workflows/1258?version=1 Riccardo Massei, Matthias Bernt fair, fair workflows, omero, rdm, workflows, bioimaging, imaging 2025-01-28 2025-03-03 1 1 7.0 param_value_from_file, tp_replace_in_line, split_file_to_collection, omero_roi_import, omero_import, omero_metadata_import, Convert characters1 Image analysis MIT 10.48546/workflowhub.workflow.1258.1 UFZ - Image Data Management and Processing Workflows True False
YOLO training and segmentation workflow https://usegalaxy.eu 751e3e2c338949c0 https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0 nfdi4bioimage, Yi Sun, Arif Khan yolo, bioimage 2025-06-16 2025-08-27 28 28 graphicsmagick_image_convert, ip_histogram_equalization, yolo_training, interactive_tool_anylabeling, json2yolosegment Visualisation, Image annotation, Data handling, Image analysis GPL-3.0-or-later True False
Voronoi segmentation with seed generation https://usegalaxy.eu 7f8ff64c5ea03a9b https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b imageanaylsis, segmentation, voronoi 2025-07-25 2025-07-25 6 6 ip_filter_standard, ip_split_image, __EXTRACT_DATASET__, graphicsmagick_image_convert, ip_threshold Image analysis MIT True False
Voronoi segmentation for Astronomy on Legacy Survey data https://usegalaxy.eu bc78c184fabcff1d https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d Even Moa Myklebust, Riccardo Massei segmentation, imageanaylsis, voronoi, astronomy 2025-05-08 2025-06-11 14 14 ip_filter_standard, ip_2d_feature_extraction, ip_split_image, ip_overlay_images, ip_convertimage, ip_binary_to_labelimage, voronoi_tessellation, astropy_fits2bitmap, __EXTRACT_DATASET__, image_math, ip_threshold, ip_histogram_equalization, colorize_labels, repeat_channels, desi_legacy_survey_astro_tool, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis MIT True False
Voronoi segmentation https://usegalaxy.eu 23030421cd9fcfb2 https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2 Even Moa Myklebust, Riccardo Massei segmentation, imageanaylsis, voronoi 2025-04-22 2025-04-25 14 14 ip_filter_standard, ip_2d_feature_extraction, ip_overlay_images, voronoi_tessellation, ip_convertimage, ip_binary_to_labelimage, image_math, ip_threshold, colorize_labels, repeat_channels, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis MIT True False
2025_Generic_Nuclei_Segmentation https://usegalaxy.eu 1ffacb28226460ac https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac Riccardo Massei imageanaylsis, segmentation, nfdi4bioimage 2024-04-22 2025-03-07 19 19 ip_filter_standard, ip_2d_feature_extraction, ip_overlay_images, ip_convertimage, ip_binary_to_labelimage, ip_threshold, ip_histogram_equalization, ip_2d_filter_segmentation_by_features, ip_count_objects Visualisation, Image annotation, Data handling, Image analysis MIT True False
Manual Threshold Tester https://usegalaxy.eu e87e726b57f1a875 https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875 Riccardo Massei threshold, preprocessing, imageanalysis 2024-04-23 2024-05-05 4 4 tp_split_on_column, ip_threshold, param_value_from_file Image analysis True False
Bladder MSI WF6: annotating potential identities https://usegalaxy.eu e573c6b697524e3a https://usegalaxy.eu/published/workflow?id=e573c6b697524e3a Melanie Föll bladder_msi, ms_imaging, shared 2021-08-09 2021-08-09 1 1 datamash_ops, join_files_on_column_fuzzy, Remove beginning1, cat1 MIT True False
Bladder MSI WF5: visualization https://usegalaxy.eu fb233e418d015649 https://usegalaxy.eu/published/workflow?id=fb233e418d015649 Melanie Föll bladder_msi, ms_imaging, shared 2021-06-22 2021-08-09 9 9 cardinal_mz_images, Show beginning1, cardinal_preprocessing, cardinal_spectra_plots, cardinal_filtering, Filter1 MIT True False
Bladder MSI WF4: classification infiltrating vs. non-infiltrating https://usegalaxy.eu 9e497c5c9e64d9b3 https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3 Melanie Föll bladder_msi, ms_imaging, shared 2021-08-02 2021-08-09 6 6 tp_easyjoin_tool, sklearn_train_test_split, param_value_from_file, datamash_ops, cat1, cardinal_classification, cardinal_filtering, addName, Remove beginning1, Filter1 MIT True False
Bladder MSI WF3: classification tumor vs. stroma https://usegalaxy.eu f4a55ef0d4c2cd97 https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97 Melanie Föll bladder_msi, ms_imaging, shared 2021-07-27 2021-08-09 8 8 tp_easyjoin_tool, sklearn_train_test_split, param_value_from_file, Cut1, datamash_ops, cat1, tp_sorted_uniq, cardinal_classification, cardinal_filtering, addName, Remove beginning1, Filter1 MIT True False
Bladder MSI WF2: data handling and preprocessing https://usegalaxy.eu 7ee6976f69131683 https://usegalaxy.eu/published/workflow?id=7ee6976f69131683 Melanie Föll bladder_msi, ms_imaging, shared 2021-07-22 2021-08-09 9 9 maldi_quant_peak_detection, cardinal_quality_report, cardinal_preprocessing, cardinal_filtering, __BUILD_LIST__, cardinal_data_exporter, cardinal_combine, Filter1 MIT True False
Bladder MSI WF1: Co-registration and ROI extraction https://usegalaxy.eu 03e8b0d3dcedc092 https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092 Melanie Föll bladder_msi, ms_imaging, shared 2021-07-22 2021-08-09 12 12 ip_landmark_registration, tp_easyjoin_tool, cardinal_mz_images, tp_replace_in_line, Cut1, datamash_ops, graphicsmagick_image_convert, ip_coordinates_of_roi, ip_scale_image, cat1, tp_cat, ip_projective_transformation_points, imagecoordinates_flipaxis, addName, Remove beginning1, ip_viz_overlay_moving_and_fixed_image Image analysis MIT True False
Co-registration of MSI image and real image with landmarks https://usegalaxy.eu 64bb7a64877034dc https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc massspectrometryimaging 2019-04-11 2020-06-22 11 11 ip_landmark_registration, graphicsmagick_image_convert, ip_coordinates_of_roi, ip_scale_image, tp_cat, ip_projective_transformation_points, imagecoordinates_flipaxis, addName, Remove beginning1, ip_viz_overlay_moving_and_fixed_image Image analysis True False
Bruker spotlist conversion to annotation tabular file https://usegalaxy.eu 739214a6dfa194e1 https://usegalaxy.eu/published/workflow?id=739214a6dfa194e1 massspectrometryimaging 2019-01-30 2019-04-11 14 14 tp_split_on_column, Remove beginning1, tp_replace_in_line, Cut1 True False
Bruker ROI.xml conversion to annotation tabular file https://usegalaxy.eu 1f3f6757de60d3cf https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf massspectrometryimaging 2019-01-03 2019-04-11 14 14 tp_replace_in_line, xpath, Cut1, tp_cat, __RELABEL_FROM_FILE__, tp_split_on_column, addName True False
scan for C/D-box sequences with segmentation-fold https://usegalaxy.eu 3b717623054d5125 https://usegalaxy.eu/published/workflow?id=3b717623054d5125 rna, c/d-box, snorna 2019-01-23 2019-01-23 0 0 smf_utils_find-boxes, smf_utils_filter-by-energy, smf_utils_estimate-energy, smf_utils_extract-boxed-sequences, smf_utils_fix-fasta-headers True False