|
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_2d_feature_extraction, ip_convertimage, image_math, ip_threshold, ip_filter_standard, desi_legacy_survey_astro_tool, repeat_channels, ip_binary_to_labelimage, ip_histogram_equalization, colorize_labels, ip_count_objects, astropy_fits2bitmap, voronoi_tessellation, ip_split_image, ip_overlay_images, __EXTRACT_DATASET__ |
Data handling, Image analysis, Visualisation, Image annotation |
Physics |
MIT |
10.48546/workflowhub.workflow.1730.1 |
EuroScienceGateway |
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 |
ip_threshold, iscc_sum, ip_split_image, __EXTRACT_DATASET__, iscc_sum_verify, param_value_from_file |
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 |
libcarna_render, biapy |
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_2d_feature_extraction, interactive_tool_qupath, ip_imageinfo, ip_points_to_label, graphicsmagick_image_convert, ip_split_image |
Data handling, Image analysis, Visualisation, Image annotation |
|
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 |
json2yolosegment, yolo_training, interactive_tool_anylabeling, graphicsmagick_image_convert, ip_histogram_equalization |
Visualisation, Image analysis, Data handling, Image annotation |
|
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_threshold, ip_imageinfo, ip_binary_to_labelimage, ip_count_objects, ip_overlay_images, ip_histogram_equalization, ip_filter_standard |
Data handling, Image analysis, Visualisation, Image annotation |
|
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 |
unzip, ip_points_to_label, ip_spot_detection_2d, ip_overlay_images, ip_histogram_equalization, idr_download_by_ids |
Data handling, Image analysis, Visualisation, Image annotation |
|
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 |
image_math, ip_threshold, bioimage_inference, ip_binary_to_labelimage, ip_overlay_images, ip_split_image, __EXTRACT_DATASET__ |
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_2d_feature_extraction, ip_convertimage, image_math, ip_threshold, repeat_channels, ip_binary_to_labelimage, colorize_labels, ip_count_objects, voronoi_tessellation, ip_overlay_images, ip_filter_standard |
Data handling, Image analysis, Visualisation, Image annotation |
|
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_threshold, collapse_dataset, tp_split_on_column, ip_histogram_equalization, ip_filter_standard, ip_segmetrics, param_value_from_file |
Data handling, Image analysis, Visualisation, Image annotation |
|
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 |
ip_convertimage, scimap_mcmicro_to_anndata, ashlar, vitessce_spatial, unet_coreograph, rename_tiff_channels, quantification, basic_illumination, scimap_phenotyping, mesmer |
|
|
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_2d_feature_extraction, ip_threshold, ip_binary_to_labelimage, ip_2d_filter_segmentation_by_features, ip_filter_standard |
Data handling, Image analysis, Visualisation, Image annotation |
|
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_convert_objects_to_image, cp_measure_image_area_occupied, cp_measure_object_intensity, cp_common, cp_measure_image_quality, cp_enhance_or_suppress_features, cp_mask_image, cp_cellprofiler, cp_display_data_on_image, cp_measure_image_intensity, cp_measure_object_size_shape, cp_measure_granularity, cp_gray_to_color, cp_image_math, cp_identify_primary_objects, cp_relate_objects, cp_save_images, cp_export_to_spreadsheet, cp_measure_texture, idr_download_by_ids |
Image analysis, Quantification, Parsing |
|
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_measure_object_intensity, cp_identify_primary_objects, cp_overlay_outlines, unzip, cp_tile, cp_save_images, cp_measure_object_size_shape, cp_track_objects, cp_export_to_spreadsheet, cp_cellprofiler, cp_color_to_gray, cp_common |
Image analysis, Quantification, Parsing |
|
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_measure_object_intensity, cp_identify_primary_objects, cp_overlay_outlines, unzip, cp_tile, cp_save_images, cp_measure_object_size_shape, cp_track_objects, cp_export_to_spreadsheet, cp_cellprofiler, cp_color_to_gray, cp_common |
Image analysis, Quantification, Parsing |
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_convert_objects_to_image, cp_measure_image_area_occupied, cp_measure_object_intensity, cp_common, cp_measure_image_quality, cp_enhance_or_suppress_features, cp_mask_image, cp_cellprofiler, cp_display_data_on_image, cp_measure_image_intensity, cp_measure_object_size_shape, cp_measure_granularity, cp_gray_to_color, cp_image_math, cp_identify_primary_objects, cp_relate_objects, cp_save_images, cp_export_to_spreadsheet, cp_measure_texture, idr_download_by_ids |
Image analysis, Quantification, Parsing |
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 |
ip_2d_feature_extraction, ip_convertimage, collection_element_identifiers, ip_threshold, imagej2_analyze_particles_binary, omero_metadata_import, Convert characters1, tp_awk_tool, omero_roi_import, split_file_to_collection, ip_binary_to_labelimage, omero_filter, omero_import, ip_histogram_equalization, tp_find_and_replace, ip_filter_standard, tp_replace_in_column, param_value_from_file |
Data handling, Image analysis, Visualisation, Image annotation |
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 |
tp_replace_in_line, omero_metadata_import, Convert characters1, omero_roi_import, split_file_to_collection, omero_import, param_value_from_file |
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 |
|
json2yolosegment, yolo_training, interactive_tool_anylabeling, graphicsmagick_image_convert, ip_histogram_equalization |
Visualisation, Image analysis, Data handling, Image annotation |
|
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_threshold, ip_filter_standard, graphicsmagick_image_convert, ip_split_image, __EXTRACT_DATASET__ |
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_2d_feature_extraction, ip_convertimage, image_math, ip_threshold, ip_filter_standard, desi_legacy_survey_astro_tool, repeat_channels, ip_binary_to_labelimage, ip_histogram_equalization, colorize_labels, ip_count_objects, astropy_fits2bitmap, voronoi_tessellation, ip_split_image, ip_overlay_images, __EXTRACT_DATASET__ |
Data handling, Image analysis, Visualisation, Image annotation |
|
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_2d_feature_extraction, ip_convertimage, image_math, ip_threshold, repeat_channels, ip_binary_to_labelimage, colorize_labels, ip_count_objects, voronoi_tessellation, ip_overlay_images, ip_filter_standard |
Data handling, Image analysis, Visualisation, Image annotation |
|
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_2d_feature_extraction, ip_convertimage, ip_threshold, ip_binary_to_labelimage, ip_count_objects, ip_2d_filter_segmentation_by_features, ip_histogram_equalization, ip_overlay_images, ip_filter_standard |
Data handling, Image analysis, Visualisation, Image annotation |
|
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 |
|
ip_threshold, tp_split_on_column, 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 |
|
cat1, join_files_on_column_fuzzy, Remove beginning1, datamash_ops |
|
|
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_filtering, cardinal_mz_images, Filter1, Show beginning1, cardinal_spectra_plots, cardinal_preprocessing |
|
|
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 |
|
sklearn_train_test_split, cardinal_filtering, Remove beginning1, tp_easyjoin_tool, Filter1, addName, cat1, datamash_ops, cardinal_classification, param_value_from_file |
|
|
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 |
|
sklearn_train_test_split, tp_sorted_uniq, cardinal_filtering, Cut1, Remove beginning1, tp_easyjoin_tool, addName, cat1, Filter1, datamash_ops, cardinal_classification, param_value_from_file |
|
|
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 |
|
cardinal_quality_report, cardinal_combine, cardinal_filtering, maldi_quant_peak_detection, __BUILD_LIST__, cardinal_data_exporter, Filter1, cardinal_preprocessing |
|
|
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_projective_transformation_points, tp_replace_in_line, ip_coordinates_of_roi, imagecoordinates_flipaxis, Cut1, graphicsmagick_image_convert, Remove beginning1, cardinal_mz_images, ip_landmark_registration, addName, ip_viz_overlay_moving_and_fixed_image, tp_cat, tp_easyjoin_tool, ip_scale_image, cat1, datamash_ops |
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_projective_transformation_points, ip_coordinates_of_roi, imagecoordinates_flipaxis, graphicsmagick_image_convert, ip_viz_overlay_moving_and_fixed_image, Remove beginning1, ip_landmark_registration, addName, tp_cat, ip_scale_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_replace_in_line, Remove beginning1, Cut1, tp_split_on_column |
|
|
|
|
|
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, Cut1, tp_split_on_column, addName, tp_cat, xpath, __RELABEL_FROM_FILE__ |
|
|
|
|
|
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_filter-by-energy, smf_utils_fix-fasta-headers, smf_utils_estimate-energy, smf_utils_find-boxes, smf_utils_extract-boxed-sequences |
|
|
|
|
|
True |
False |