|
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 |
image_math, ip_overlay_images, ip_2d_feature_extraction, __EXTRACT_DATASET__, ip_split_image, desi_legacy_survey_astro_tool, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, repeat_channels, astropy_fits2bitmap, ip_filter_standard, voronoi_tessellation, colorize_labels |
Data handling, Image annotation, Image analysis, Visualisation |
Physics |
MIT |
10.48546/workflowhub.workflow.1730.1 |
EuroScienceGateway |
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_overlay_images, ip_imageinfo, ip_histogram_equalization, ip_binary_to_labelimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
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_points_to_label, ip_overlay_images, ip_histogram_equalization, idr_download_by_ids, unzip, ip_spot_detection_2d |
Data handling, Image annotation, Image analysis, Visualisation |
|
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_overlay_images, ip_threshold, __EXTRACT_DATASET__, ip_split_image, ip_binary_to_labelimage, 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 |
image_math, ip_overlay_images, ip_2d_feature_extraction, ip_threshold, ip_convertimage, ip_count_objects, ip_binary_to_labelimage, repeat_channels, ip_filter_standard, voronoi_tessellation, colorize_labels |
Data handling, Image annotation, Image analysis, Visualisation |
|
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 |
collapse_dataset, ip_histogram_equalization, param_value_from_file, tp_split_on_column, ip_threshold, ip_segmetrics, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
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 |
rename_tiff_channels, unet_coreograph, ashlar, basic_illumination, ip_convertimage, mesmer, quantification, scimap_phenotyping, scimap_mcmicro_to_anndata, vitessce_spatial |
|
|
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_binary_to_labelimage, ip_2d_filter_segmentation_by_features, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
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_mask_image, cp_convert_objects_to_image, cp_common, cp_image_math, cp_export_to_spreadsheet, cp_measure_object_intensity, cp_measure_granularity, cp_measure_object_size_shape, cp_relate_objects, idr_download_by_ids, cp_measure_image_area_occupied, cp_gray_to_color, cp_save_images, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_measure_image_quality, cp_cellprofiler, cp_measure_texture, cp_measure_image_intensity, 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_measure_object_intensity, cp_overlay_outlines, cp_measure_object_size_shape, cp_identify_primary_objects, unzip, cp_common, cp_export_to_spreadsheet, cp_track_objects, cp_color_to_gray, cp_save_images, cp_tile, cp_cellprofiler |
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_measure_object_intensity, cp_overlay_outlines, cp_measure_object_size_shape, cp_identify_primary_objects, unzip, cp_common, cp_export_to_spreadsheet, cp_track_objects, cp_color_to_gray, cp_save_images, cp_tile, cp_cellprofiler |
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_mask_image, cp_convert_objects_to_image, cp_common, cp_image_math, cp_export_to_spreadsheet, cp_measure_object_intensity, cp_measure_granularity, cp_measure_object_size_shape, cp_relate_objects, idr_download_by_ids, cp_measure_image_area_occupied, cp_gray_to_color, cp_save_images, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_measure_image_quality, cp_cellprofiler, cp_measure_texture, cp_measure_image_intensity, 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 |
collection_element_identifiers, ip_2d_feature_extraction, ip_histogram_equalization, omero_import, tp_awk_tool, split_file_to_collection, ip_binary_to_labelimage, ip_convertimage, imagej2_analyze_particles_binary, param_value_from_file, omero_metadata_import, omero_roi_import, tp_replace_in_column, ip_threshold, Convert characters1, omero_filter, tp_find_and_replace, ip_filter_standard |
Image analysis, Image annotation, Data handling, Visualisation |
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, omero_import, omero_roi_import, split_file_to_collection, omero_metadata_import, tp_replace_in_line, 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 |
|
ip_histogram_equalization, graphicsmagick_image_convert, json2yolosegment, yolo_training, interactive_tool_anylabeling |
Visualisation, Data handling, Image analysis, 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 |
|
__EXTRACT_DATASET__, graphicsmagick_image_convert, ip_split_image, ip_threshold, ip_filter_standard |
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 |
|
image_math, ip_overlay_images, ip_2d_feature_extraction, __EXTRACT_DATASET__, ip_split_image, desi_legacy_survey_astro_tool, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, repeat_channels, astropy_fits2bitmap, ip_filter_standard, voronoi_tessellation, colorize_labels |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |
|
Segmentation and counting of cell nuclei in fluorescence microscopy images (release v0.1) |
https://usegalaxy.eu |
6fbd9b2274c62ebe |
https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe |
Leonid Kostrykin |
|
2024-03-07 |
2025-04-25 |
1 |
1 |
|
ip_overlay_images, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |
|
Segmentation and counting of cell nuclei in fluorescence microscopy images (release v0.2) |
https://usegalaxy.eu |
dc8b78d093be59ae |
https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae |
Leonid Kostrykin |
|
2024-11-21 |
2025-04-25 |
1 |
1 |
|
ip_overlay_images, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
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 |
|
image_math, ip_overlay_images, ip_2d_feature_extraction, ip_threshold, ip_convertimage, ip_count_objects, ip_binary_to_labelimage, repeat_channels, ip_filter_standard, voronoi_tessellation, colorize_labels |
Data handling, Image annotation, Image analysis, Visualisation |
|
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_overlay_images, ip_2d_feature_extraction, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_2d_filter_segmentation_by_features, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |
|
Nuclei Segmentation Example |
https://usegalaxy.eu |
7d7550ce7004d71e |
https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e |
Michele Bortolomeazzi |
imageanaylsis |
2024-09-11 |
2024-09-13 |
19 |
19 |
|
ip_overlay_images, ip_histogram_equalization, idr_download_by_ids, __EXTRACT_DATASET__, ip_binary_to_labelimage, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
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 |
|
imagecoordinates_flipaxis, Remove beginning1, graphicsmagick_image_convert, ip_scale_image, ip_viz_overlay_moving_and_fixed_image, ip_landmark_registration, ip_projective_transformation_points, ip_coordinates_of_roi, addName, tp_cat |
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, tp_split_on_column, 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 |
|
Cut1, xpath, tp_split_on_column, tp_replace_in_line, __RELABEL_FROM_FILE__, addName, tp_cat |
|
|
|
|
|
True |
False |
|
Segmentation and counting of cell nuclei in fluorescence microscopy images (release v0.1) |
https://usegalaxy.org |
a8e39acc103c3d6b |
https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b |
Leonid Kostrykin |
|
2024-10-31 |
2025-04-25 |
1 |
1 |
|
ip_overlay_images, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |
|
Segmentation and counting of cell nuclei in fluorescence microscopy images (release v0.2) |
https://usegalaxy.org |
d47cddc372c88094 |
https://usegalaxy.org/published/workflow?id=d47cddc372c88094 |
Leonid Kostrykin |
|
2024-11-21 |
2025-04-25 |
1 |
1 |
|
ip_overlay_images, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |
|
Segmentation and counting of cell nuclei in fluorescence microscopy images (release v0.2) |
https://usegalaxy.org.au |
8e28c3b252062b3b |
https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b |
Leonid Kostrykin |
|
2024-11-21 |
2025-04-25 |
1 |
1 |
|
ip_overlay_images, ip_histogram_equalization, ip_binary_to_labelimage, ip_convertimage, ip_count_objects, ip_threshold, ip_filter_standard |
Data handling, Image annotation, Image analysis, Visualisation |
|
MIT |
|
|
True |
False |