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{ "count": 9480, "next": "?page=2", "previous": null, "list": [ { "name": "oct-to-tiff", "description": "A command line tool for converting optical coherence tomography angiography (OCTA) data.", "homepage": "https://github.com/camlloyd/oct-to-tiff", "biotoolsID": "oct-to-tiff", "biotoolsCURIE": "biotools:oct-to-tiff", "version": [ "0.6.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2025-12-08T13:54:29.684754Z", "lastUpdate": "2025-12-08T14:38:17.484605Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mapping-based Genome Size Estimation", "description": "Mapping-based Genome Size Estimation (MGSE) predicts the size of a genome based on a (short) read mapping to an existing genome assembly. Low complexity sequences are often collapsed in a genome assembly thus the assembly size is smaller than the genome size. The actual copy number of sequences in the assembly is identified based on the coverage (sequencing depth) which allows the calculation of a genome size.", "homepage": "https://github.com/bpucker/MGSE", "biotoolsID": "mgse", "biotoolsCURIE": "biotools:mgse", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://doi.org/10.1186/s12864-025-11640-8", "type": [ "Repository" ], "note": "Publication in BMC Genomics" } ], "download": [ { "url": "https://github.com/bpucker/MGSE", "type": "Downloads page", "note": "MGSE is available on GitHub", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1186/s12864-025-11640-8", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mapping-based genome size estimation", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Boas Pucker", "email": null, "url": "https://www.pbb.uni-bonn.de", "orcidid": "https://orcid.org/0000-0002-3321-7471", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "bpucker", "additionDate": "2021-01-02T12:42:50Z", "lastUpdate": "2025-12-06T16:20:42.941757Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Quality Assessment metrics (IQA) for XNAT platform", "description": "Docker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of preclinical and clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.", "homepage": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "biotoolsID": "image_quality_assessment_metrics_iqa_for_xnat_platform", "biotoolsCURIE": "biotools:image_quality_assessment_metrics_iqa_for_xnat_platform", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "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_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "MATLAB" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/17goRA76d9vViR93HbhIcjPPxsCdtGhS9/edit?usp=sharing&ouid=114076787312989347088&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Feriel Romdhane", "email": "ferielromdhane@yahoo.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-5854-9341", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Euro-BioImaging ERIC", "email": "preclinicaldata@eurobioimaging.eu", "url": "https://www.eurobioimaging.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "National Research Council", "email": null, "url": "https://www.ibb.cnr.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Feriel", "additionDate": "2025-10-15T07:25:34.085350Z", "lastUpdate": "2025-12-05T14:40:30.073701Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Duplicates Checker", "description": "Detects duplicate or visually similar DICOM series using a tiered approach that combines metadata analysis, hash-based comparison, and pixel-level similarity metrics.\nIdeal for:\n1. High-level series comparison and classification, and\n2. Detecting duplicates even after post-processing (e.g., denoising, filtering).\n\nFor scenarios requiring strict, image-level deduplication based solely on pixel content, fully agnostic to metadata changes introduced through anonymization, consider using [link]", "homepage": "https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies", "biotoolsID": "dicom_image_similarity-duplicate_checker", "biotoolsCURIE": "biotools:dicom_image_similarity-duplicate_checker", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "data_integration_quality_check_tool_diqct", "type": "includedIn" } ], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "eucaim" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "difoto", "additionDate": "2025-05-28T23:55:08.439649Z", "lastUpdate": "2025-12-04T18:00:23.742140Z", "editPermission": { "type": "group", "authors": [ "authEucaim" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR EVA for EUCAIM", "description": "FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_0.3", "EUCAIM_plugin_0.3.1", "EUCAIM_plugin_0.4.0", "EUCAIM_0.4.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1052", "term": "URL" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out" } ], "toolType": [ "Plug-in", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "type": [ "Repository" ], "note": "Repository for FAIR EVA, without the EUCAIM specific plugin" } ], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "General" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." }, { "url": "https://gitlabpages.ifca.es/fair-eva-guide-608baa/", "type": [ "User manual" ], "note": "Wiki page with FAIR EVA for EUCAIM specific instructions." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": null, "abstract": null, "date": null, "citationCount": 0, "authors": [], "journal": null } } ], "credit": [ { "name": "Fernando Aguilar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9462-4831", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor" ], "note": "Creator and devloper of the main package FAIR EVA.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." }, { "name": "David Rodríguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9160-5106", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": "Developer of the EUCAIM plugin." }, { "name": "Inés Victoria", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0003-7950-3937", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Developer of the EUCAIM plugin." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-12-04T10:57:20.901575Z", "editPermission": { "type": "group", "authors": [ "ines.ifca", "davrodgon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AggreProt", "description": "AggreProt is a web server to predict and engineer protein aggregation that provide a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.", "homepage": "https://loschmidt.chemi.muni.cz/aggreprot/", "biotoolsID": "aggreprotv1.0", "biotoolsCURIE": "biotools:aggreprotv1.0", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Java", "JavaScript" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkae420", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "AggreProt: A web server for predicting and engineering aggregation prone regions in proteins", "abstract": "", "date": "2024-07-05T00:00:00Z", "citationCount": 17, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Joan Planas-Iglesias", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Simeon Borko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jiří Damborský", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "David Bednář", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "m.musil", "additionDate": "2025-12-03T14:05:12.102283Z", "lastUpdate": "2025-12-03T14:05:12.105361Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SoluProtMutsupDB", "description": "A manually curated database of protein solubility changes upon mutations.", "homepage": "http://loschmidt.chemi.muni.cz/soluprotmutdb", "biotoolsID": "soluprotmutsupdb", "biotoolsCURIE": "biotools:soluprotmutsupdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0409", "term": "Protein solubility prediction" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/J.CSBJ.2022.11.009", "pmid": "36420168", "pmcid": "PMC9678803", "type": [], "version": null, "note": null, "metadata": { "title": "SoluProtMutDB: A manually curated database of protein solubility changes upon mutations", "abstract": "© 2022 The Author(s)Protein solubility is an attractive engineering target primarily due to its relation to yields in protein production and manufacturing. Moreover, better knowledge of the mutational effects on protein solubility could connect several serious human diseases with protein aggregation. However, we have limited understanding of the protein structural determinants of solubility, and the available data have mostly been scattered in the literature. Here, we present SoluProtMutDB – the first database containing data on protein solubility changes upon mutations. Our database accommodates 33 000 measurements of 17 000 protein variants in 103 different proteins. The database can serve as an essential source of information for the researchers designing improved protein variants or those developing machine learning tools to predict the effects of mutations on solubility. The database comprises all the previously published solubility datasets and thousands of new data points from recent publications, including deep mutational scanning experiments. Moreover, it features many available experimental conditions known to affect protein solubility. The datasets have been manually curated with substantial corrections, improving suitability for machine learning applications. The database is available at loschmidt.chemi.muni.cz/soluprotmutdb.", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Velecky J." }, { "name": "Hamsikova M." }, { "name": "Stourac J." }, { "name": "Musil M." }, { "name": "Damborsky J." }, { "name": "Bednar D." }, { "name": "Mazurenko S." } ], "journal": "Computational and Structural Biotechnology Journal" } } ], "credit": [ { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Stanislav Mazurenko", "email": "mazurenko@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jan Velecký", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Marie Hamsikova", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "velda", "additionDate": "2023-01-25T22:49:31.072923Z", "lastUpdate": "2025-12-03T12:49:50.125351Z", "editPermission": { "type": "group", "authors": [ "velda", "m.musil" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "AggreProt", "description": "AggreProt is a web server to predict and engineer protein aggregation that provides protein aggregation propensity profile. 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Multi-criteria scoring provides personalized pipeline recommendations from eight production-ready workflows (STAR-RSEM-DESeq2, Salmon-edgeR, Kallisto-Sleuth, etc.) in 30 seconds with clear reasoning. 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Based on MITK, there is the MITK Workbench, a powerful and free application to view, process, and segment medical images.", "homepage": "https://www.mitk.org/", "biotoolsID": "mitk", "biotoolsCURIE": "biotools:mitk", "version": [ "v2023.04" ], "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_3551", "term": "nrrd" }, { "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_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workbench", "Desktop application", "Library" ], "topic": [], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C++" ], "license": "BSD-3-Clause", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/MITK/MITK/", "type": [ "Repository" ], "note": null }, { "url": "https://lists.sourceforge.net/lists/listinfo/mitk-users", "type": [ "Mailing list" ], "note": "If you have any questions related to the use of or the development with MITK, please use the official mailing list.\n\nNote that you have to subscribe to the mailing list in order to send mails" } ], "download": [ { "url": "https://www.mitk.org/wiki/Downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://docs.mitk.org/2023.04/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.media.2005.04.005", "pmid": "15896995", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit", "abstract": "Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org) © 2005 Elsevier B.V. All rights reserved.", "date": "2005-12-01T00:00:00Z", "citationCount": 378, "authors": [ { "name": "Wolf I." }, { "name": "Vetter M." }, { "name": "Wegner I." }, { "name": "Bottger T." }, { "name": "Nolden M." }, { "name": "Schobinger M." }, { "name": "Hastenteufel M." }, { "name": "Kunert T." }, { "name": "Meinzer H.-P." } ], "journal": "Medical Image Analysis" } }, { "doi": "10.1007/s11548-013-0840-8", "pmid": "23588509", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit: Challenges and advances: 10 years of open-source development", "abstract": "Purpose: The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. Methods: MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. Results: MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. Conclusions: MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research. © 2013 CARS.", "date": "2013-01-01T00:00:00Z", "citationCount": 354, "authors": [ { "name": "Nolden M." }, { "name": "Zelzer S." }, { "name": "Seitel A." }, { "name": "Wald D." }, { "name": "Muller M." }, { "name": "Franz A.M." }, { "name": "Maleike D." }, { "name": "Fangerau M." }, { "name": "Baumhauer M." }, { "name": "Maier-Hein L." }, { "name": "Maier-Hein K.H." }, { "name": "Meinzer H.-P." }, { "name": "Wolf I." } ], "journal": "International Journal of Computer Assisted Radiology and Surgery" } } ], "credit": [ { "name": "German Cancer Research Center (DKFZ)", "email": null, "url": "https://www.dkfz.de/de", "orcidid": null, "gridid": "grid.7497.d", "rorid": "04cdgtt98", "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "sschaum", "additionDate": "2023-06-26T12:38:15.108087Z", "lastUpdate": "2025-11-28T09:27:43.812008Z", "editPermission": { "type": "group", "authors": [ "ASHISR" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FTAG-Finder", "description": "Families and TAG Finder: a Snakemake workflow to identify gene families and detect Tandemly Arrayed Genes.", "homepage": "https://gitlab.com/sortion/FTAG-Finder", "biotoolsID": "ftag-finder", "biotoolsCURIE": "biotools:ftag-finder", "version": [ "0.1.0" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "mmseqs2", "type": "uses" }, { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "mcl", "type": "uses" } ], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "AWK", "C", "Bash", "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/sortion/FTAG-Finder", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/sortion/FTAG-Finder/-/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://gitlab.com/sortion/FTAG-Finder/-/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Carène Rizzon", "email": null, "url": "http://www.math-evry.cnrs.fr/members/crizzon/welcome", "orcidid": "https://orcid.org/0000-0003-1194-4130", "gridid": null, "rorid": "03jca6281", "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Samuel Ortion", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0001-0971-497X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "sortion", "additionDate": "2025-11-27T10:42:10.165590Z", "lastUpdate": "2025-11-27T10:42:10.168319Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "South Green Genome Hubs", "description": "The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. 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The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.", "homepage": "https://github.com/Feriel87/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "biotoolsID": "nlmced_filter", "biotoolsCURIE": "biotools:nlmced_filter", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "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_3579", "term": "JPG" }, { "uri": "http://edamontology.org/format_3626", "term": "MAT" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python", "MATLAB" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/Denoising-CEST-MRI/tree/main/NLmCED_Filter", "type": [ "Repository" ], "note": "Github Link" } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1kxN0Jrn6xukAi6kVSmBdo1GmfkXNZ-5B/edit?usp=sharing&ouid=114076787312989347088&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1504/IJCVR.2018.090012", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A new method for three-dimensional magnetic resonance images denoising", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 3, "authors": [], "journal": "International Journal of Computational Vision and Robotics" } }, { "doi": "10.1002/mrm.28676", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Evaluation of a similarity anisotropic diffusion denoising approach for improving in vivo CEST-MRI tumor pH imaging", "abstract": "", "date": "2021-06-01T00:00:00Z", "citationCount": 20, "authors": [], "journal": "Magnetic Resonance in Medicine" } } ], "credit": [ { "name": "Feriel Romdhane", "email": "ferielromdhane@yahoo.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-5854-9341", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Feriel", "additionDate": "2023-07-13T08:14:40.190855Z", "lastUpdate": "2025-11-19T08:21:46.074848Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ACPred", "description": "Computational Tool for the Prediction and Analysis of Anticancer Peptides.", "homepage": "http://codes.bio/acpred/", "biotoolsID": "ACPred", "biotoolsCURIE": "biotools:ACPred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0252", "term": "Peptide immunogenicity prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Unlicense", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Shoombuatong2527/acpred", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/chaninlab/acpred-webserver", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/MOLECULES24101973", "pmid": "31121946", "pmcid": "PMC6571645", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ACPred: A computational tool for the prediction and analysis of anticancer peptides", "abstract": "© 2019 MDPI AG. All rights reserved.Anticancer peptides (ACPs) have emerged as a new class of therapeutic agent for cancer treatment due to their lower toxicity as well as greater efficacy, selectivity and specificity when compared to conventional small molecule drugs. However, the experimental identification of ACPs still remains a time-consuming and expensive endeavor. Therefore, it is desirable to develop and improve upon existing computational models for predicting and characterizing ACPs. In this study, we present a bioinformatics tool called the ACPred, which is an interpretable tool for the prediction and characterization of the anticancer activities of peptides. ACPred was developed by utilizing powerful machine learning models (support vector machine and random forest) and various classes of peptide features. It was observed by a jackknife cross-validation test that ACPred can achieve an overall accuracy of 95.61% in identifying ACPs. In addition, analysis revealed the following distinguishing characteristics that ACPs possess: (i) hydrophobic residue enhances the cationic properties of α-helical ACPs resulting in better cell penetration; (ii) the amphipathic nature of the α-helical structure plays a crucial role in its mechanism of cytotoxicity; and (iii) the formation of disulfide bridges on β-sheets is vital for structural maintenance which correlates with its ability to kill cancer cells. Finally, for the convenience of experimental scientists, the ACPred web server was established and made freely available online.", "date": "2019-01-01T00:00:00Z", "citationCount": 42, "authors": [ { "name": "Schaduangrat N." }, { "name": "Nantasenamat C." }, { "name": "Prachayasittikul V." }, { "name": "Shoombuatong W." } ], "journal": "Molecules" } } ], "credit": [ { "name": "Watshara Shoombuatong", "email": "watshara.sho@mahidol.ac.th", "url": null, "orcidid": "https://orcid.org/0000-0002-3394-8709", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:07:09Z", "lastUpdate": "2025-11-17T12:41:12.905009Z", "editPermission": { "type": "group", "authors": [ "ningning" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetFamily", "description": "Web application designed for the identification of regulated metabolite families. 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However, alternative data sources can also be used as described in the MetFamily input specification.\nPrincipal component analysis of MS1 data and hierarchical cluster analysis of MS/MS data can be exported.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "Freeware", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01569", "type": [ "User manual" ], "note": "Is available in the 'About' tab of the web app (http://msbi.ipb-halle.de/MetFamily/) and as supplement of the publication." } ], "publication": [ { "doi": "10.1021/acs.analchem.6b01569", "pmid": "27452369", "pmcid": null, "type": [ "Primary" ], 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Spacedust adapts the fast and sensitive structure comparisons of Foldseek and homology search capabilities of MMseqs2. 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