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{ "count": 32977, "next": "?page=2", "previous": null, "list": [ { "name": "MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)", "description": "This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK", "type": [ "User manual" ], "note": null }, { "url": "https://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Diana Veiga Canuto", "email": "dianaveigac@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6048-2940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Support", "Documentor", "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Documentor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:08:44.174795Z", "lastUpdate": "2026-04-30T11:37:29.346721Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus: Deployed", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "2.0.0", "2.1.0", "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Holders (ingestion-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n -v \"<config_path>:/config\" \\\n harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Users (processing-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest \\\n /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Holders" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Users" } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": "Container file", "note": "EUCAIM user needed", "version": "2.1.0" } ], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3", "type": [ "Training material" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Documentor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2026-04-30T11:36:53.934680Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)", "description": "The tool is designed to perform a customisable image pre-processing to reduce noise and inhomogeneity field effect, thus improving image quality and reproducibility of radiomics features. This tool consists of two independent steps: one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means (NLM)), and another for the ANTs N4 and another for the ANT's N4 bias correction filter. The parameter configuration of this tool has been optimised for TW1, T2W, DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but it can also be configured with some of their parameters using a JSON parameter configuration file.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tab", "biotoolsID": "denoising-inhomogeneity_correction_tool", "biotoolsCURIE": "biotools:denoising-inhomogeneity_correction_tool", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run -it --rm --name container_name -v \"<input_path>:/input\" -v \"<output_path>:/output\" -v \"<config_path>:/config\" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0 --config /config/config.json" }, { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0 --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W --output /output --series_number 2000 --series_description_suffix \"_harmonized\" --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size 50 --n4_iterations 50 30 --shrink_factor 2" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-021-00512-8", "pmid": "34505958", "pmcid": "PMC8554919", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/s41747-020-00150-9", "pmid": "32246291", "pmcid": "PMC7125275", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matias Fernandez-Paton", "email": "matias_fernandez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9374-1411", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Documentor", "Support" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor", "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T08:55:46.088021Z", "lastUpdate": "2026-04-30T11:36:34.414003Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)", "description": "The tool is designed to perform radiomics harmonization on large and heterogeneous datasets, where the risk of over-harmonization is present. Instead of directly applying harmonization based on predefined batch labels, the tool first identifies groups of batches that share similar characteristics through clustering of the radiomics data. It then performs harmonization using these cluster-derived labels. 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Cascaded nnU-Net v2 (anatomies) + ProLesA-Net (lesions). A three-stage pipeline that segments the whole gland (WG), peripheral zone (PZ), transition zone (TZ) and (when ADC + DWI are provided) the prostate lesions from prostate MRI. The anatomies are produced by two cascaded nnU-Net v2 models on T2; the lesion mask is produced by ProLesA-Net (Keras / TensorFlow 2.11) operating on T2 + ADC + DWI inside the WG mask", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab", "biotoolsID": "prostate_anatomies_and_lesion_automatic_segmentor", "biotoolsCURIE": "biotools:prostate_anatomies_and_lesion_automatic_segmentor", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/dicom:/input:ro -v /path/to/out:/output \\\nharbor.eucaim.cancerimage.eu/processing-tools/prostate-anatomies-and-lesion-segmentor:1.0.0 \\\n --input /input --output /output" } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "EUPL-1.2", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab", "type": "Container file", "note": null, "version": "1.0.0" }, { "url": "https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor", "type": "Source code", "note": null, "version": "1.0.0" } ], "documentation": [ { "url": "https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor", "type": [ "Quick start guide" ], "note": "Quick Start Commands for the Software, including pulling from Harbor Container Registry, input folders structure" }, { "url": "https://drive.eucaim.cancerimage.eu/s/S4qW2cRD6T5NYBQ", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/HEKfYpL9DrCqJ84", "type": [ "General" ], "note": "Video with input folders structure, docker image execution & visualisation" } ], "publication": [ { "doi": "10.1016/j.patter.2024.100992", "pmid": "39081575", "pmcid": "PMC11284496", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Foundation for Research and Technology Hellas (FORTH)", "email": null, "url": "https://www.forth.gr/en/home/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Dimitrios I. Zaridis", "email": "dimzaridis@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-2549-3887", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nikolaos Tachos", "email": "ntachos@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-8627-6352", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Dimitrios I. Fotiadis", "email": "fotiadis@uoi.gr", "url": null, "orcidid": "https://orcid.org/0000-0002-7362-5082", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "dimzaridis", "additionDate": "2026-04-30T10:37:00.214036Z", "lastUpdate": "2026-04-30T10:39:39.868431Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "protein-mosaic-q", "description": "Python library for computing the mosaic Q and Q_alt structural descriptors, which quantify the degree of spatial clustering of amino acids by chemical type (acidic, basic, polar, hydrophobic, and also special for Q_alt) in protein three-dimensional structures. Operates on PDB and mmCIF files via Biopython. Associated with the Proteins Mosaic Q Project, a citizen-science initiative gathering evidence for a conserved structural clustering pattern across proteins.", "homepage": "https://proteins-mosaic-q.org/", "biotoolsID": "protein-mosaic-q", "biotoolsCURIE": "biotools:protein-mosaic-q", "version": [ "0.3.3" ], "otherID": [], "relation": [ { "biotoolsID": "biopython", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0249", "term": "Protein geometry calculation" } ], "input": [], "output": [], "note": "Computes mosaic Q and Q_alt parameters quantifying spatial clustering of amino acids by chemical type in protein 3D structures.", "cmd": "mosaicq protein.pdb [--metric Q_alt]" } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pypi.org/project/protein-mosaic-q/", "type": [ "Software catalogue" ], "note": null }, { "url": "https://github.com/UPO-Sevilla-Fco-Javier-Lobo-Cabrera/clustering_trait_proteins", "type": [ "Repository" ], "note": null }, { "url": "https://citizenscience.eu/project/686", "type": [ "Other" ], "note": null }, { "url": "https://scistarter.org/proteins-mosaic-q-project", "type": [ "Other" ], "note": null }, { "url": "https://proteins-mosaic-q.org/", "type": [ "Other" ], "note": null }, { "url": "https://ciencia-ciudadana.es/project/392", "type": [ "Other" ], "note": null }, { "url": "https://osf.io/42kjn/overview", "type": [ "Other" ], "note": null }, { "url": "https://huggingface.co/ProteinsMosaicQ", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/protein-mosaic-q/", "type": "Software package", "note": null, "version": "0.3.3" } ], "documentation": [ { "url": "https://pypi.org/project/protein-mosaic-q/", "type": [ "General" ], "note": null }, { "url": "https://osf.io/42kjn/wiki?wiki=zmh9d", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/500025", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": "Earlier version of the manuscript. Updated version available in the project repository.", "metadata": null } ], "credit": [ { "name": "Francisco Javier Lobo-Cabrera", "email": "fjlobcab@upo.es", "url": "https://scholar.google.com/citations?user=D4NAEvEAAAAJ&hl=en", "orcidid": "https://orcid.org/0000-0002-9592-6863", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": "PhD in Biotechnology, with publications in computational biology." }, { "name": "José A. Prado-Bassas", "email": "bassas@us.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5670-5400", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Support" ], "note": "Professor at Universidad de Sevilla, Faculty of Mathematics." } ], "owner": "fjlobo", "additionDate": "2026-04-29T11:29:15.746883Z", "lastUpdate": "2026-04-29T11:29:15.749301Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Prostate zone segmentation tool", "description": "This tool automatically segments the the prostate into two zones: the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes as input a T2-weighted image and produces a segmentation in the same input format.\n\nThree datasets were used to train this model: ProstateX (n=152), Prostate158 (n=119) and ProstateNet (the ProCAncer-I dataset; n=532). We used the T2-weighted images available in each dataset and trained a standard three-class nnU-Net model with three classes: background, peripheral zone and the combination of the transition and central zones as annotated by radiologists. Using 149 cases from the three previously noted datasets, this model achieved DSC=0.81 (95% CI=[0.59, 0.92]) for PZ and 0.87 (95% CI=[0.60, 0.96]) for CZ+TZ. In a clinical validation using ProCAncer-I data, this model achieved, for PZ and TZ+CZ, DSC=0.65 and DSC=0.77, respectively, comparable to the observed between-radiologist DSC for a subset of cases (DSC=0.61 and DSC=0.73, respectively).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation", "biotoolsID": "prostate_zone_segmentation_tool", "biotoolsCURIE": "biotools:prostate_zone_segmentation_tool", "version": [], "otherID": [], "relation": [ { "biotoolsID": "nnunet", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": "Image annotation for individual DICOM and Nifti images: Please note that it is easier to mount the input and output paths path and keep `--study_path` always as `/data/input` and `--output_dir` always as `/data/output`. This way only `--series_folders` requires any change. `--series_folders` can refer both to a Nifti file (if the input is Nifti) or the a DICOM series folder.\n\nIf the input is DICOM, `--is_dicom` should be used.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict --study_path /data/input --series_folders <series-folder> --output_dir /data/output" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3442", "term": "MRI image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": "Batch image annotation for DICOM and Nifti images using dataset JSON and data directory supports two methods: using a dataset JSON and using a data directory. \n\nThe dataset JSON-based method relies on having a dataset JSON which has a list of dictionaries that follow this structure: `{\"study_path\": str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous to the previous modes. Be mindful that paths should be specified accordingly for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\nThe data directory-based method relies on having a directory structured as patient/study/series, where each series follows an nnU-Net-like convention (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should be `<series-id>_0000`. The data directory should be specified using `--data_dir` and requires the specification of an `--output_dir`.\n\nIf the input is DICOM, `--is_dicom` should be specified.", "cmd": "docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw --gpus=\"all\" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir /data/input --output_dir /data/output}}" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "Repository" ], "note": "This is the nnunet_serve repository, containing the generic nnU-Net building and serving functionalities used by the Computational Clinical Imaging Group at Champalimaud Foundation. This should also be used as documentation." }, { "url": "https://kdrive.infomaniak.com/app/share/1928123/f7bf2733-0454-47b0-a29c-0beacb51fe68", "type": [ "Other" ], "note": "Contains the EUCAIM model card for this model." } ], "download": [], "documentation": [ { "url": "https://github.com/josegcpa/nnunet_serve", "type": [ "API documentation" ], "note": "This is the repository containing all of the code together with a comprehensive README for deployment and examplar files." } ], "publication": [ { "doi": "10.1016/j.compbiomed.2024.108216", "pmid": "38442555", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": "https://josegcpa.net", "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Nickolas Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Nuno Rodrigues", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-11-07T18:15:49.962044Z", "lastUpdate": "2026-04-29T10:36:29.272637Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Immune Checkpoint Inhibitor Development Services for Cancer", "description": "Alfa Cytology provides comprehensive preclinical research and development services aimed at advancing the field of cancer therapy by facilitating the discovery and optimization of novel immune checkpoint inhibitors. 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