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  description: Best Match Tagger for removing contaminant reads from metagenomics
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  owner: m.bernt
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  - term: Metagenomics
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  cost: Free of charge
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  description: A command-line tool for differential expression analysis in quantitative
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    - data:
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    note: null
    operation:
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      - term: HTML
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      format:
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    note: null
    operation:
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    - data:
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    note: null
    operation:
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    output:
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      format:
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  language:
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  license: MIT
  link:
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    type:
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  - note: null
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  name: prolfquapp
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    metadata:
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      authors: []
      citationCount: 1
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      journal: Journal of Proteome Research
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    note: null
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    pmid: null
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    orcidid: https://orcid.org/0000-0001-5242-6060
    rorid: null
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  description: 'The tool is designed to perform harmonization at the feature-level.
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  - note: null
    type:
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  language:
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  lastUpdate: '2025-11-06T10:01:42.643613Z'
  license: MIT
  link:
  - note: null
    type:
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  - note: Link to EUCAIM's harbor
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  additionDate: '2025-10-30T11:34:24.728018Z'
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  description: 'The tool is designed to perform normalization at the image-level.
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  - note: null
    type:
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  function:
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    input:
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    note: null
    operation:
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  language:
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  lastUpdate: '2025-11-06T09:42:46.820448Z'
  license: MIT
  link:
  - note: null
    type:
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  - note: Link to EUCAIM's Harbor
    type:
    - Other
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/bio_intensity_norm/artifacts-tab
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  name: Biologically motivated normalization techniques
  operatingSystem:
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  - Mac
  - Linux
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  publication: []
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  toolType:
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  topic:
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  - term: Data visualisation
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-10-30T11:16:20.075783Z'
  biotoolsCURIE: biotools:n4_bias_filter
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  collectionID:
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  credit:
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    orcidid: https://orcid.org/0000-0001-5242-6060
    rorid: null
    typeEntity: Person
    typeRole:
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  description: 'The tool is designed to perform image pre-processing to reduce the
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  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://cbml-gitlab.ics.forth.gr/adovrou/n4biasfilter/-/tree/eucaim?ref_type=heads
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    note: null
    operation:
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    output:
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      format:
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  - cmd: null
    input:
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      format:
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    type:
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  name: N4 Bias Filter
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    metadata:
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      citationCount: 23
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  description: The Spectra package defines an efficient infrastructure for storing
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  - note: null
    type:
    - API documentation
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  toolType:
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  topic:
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  - term: Proteomics experiment
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  version: []
- accessibility: Open access
  additionDate: '2017-01-17T15:04:54Z'
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  description: Framework for processing and visualization of chromatographically separated
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  - note: Galaxy training material for LC-MS data preprocessing with XCMS
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  description: Interoperable open-source package for the calculation of standardized
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  additionDate: '2017-01-17T15:04:48Z'
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  description: This tool comprises a workflow to interactively explore metabolomics
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      citationCount: 20
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  additionDate: '2025-10-31T10:28:34.411099Z'
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  topic:
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  description: An open source research information system, used to manage, collect
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  - note: null
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    note: null
    operation:
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  homepage: https://osiris-app.de
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  language:
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  lastUpdate: '2025-11-04T14:19:23.174608Z'
  license: MIT
  link:
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  name: OSIRIS
  operatingSystem:
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  owner: JKoblitz
  publication: []
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  - term: Data management
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  - term: Database management
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  additionDate: '2025-04-15T17:42:40.968987Z'
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  cost: Free of charge (with restrictions)
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  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
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      \ Abril Martorell, València, 46026, Spain.\n3\tComputing Science Department,\
      \ Universitat Politècnica de València, Cami de Vera s/n, València, 46022, Spain."
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    note: null
    operation:
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        uri: http://edamontology.org/format_3464
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
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  language:
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  lastUpdate: '2025-11-04T13:08:53.549989Z'
  license: CC-BY-NC-ND-4.0
  link:
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    type:
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    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
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  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
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  - Linux
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  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
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  topic:
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    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
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  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
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    rorid: null
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  description: BreastDeformNet is a deep learning tool for predicting non-rigid breast
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  name: BreastDeformNet
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      journal: Proceedings - International Symposium on Biomedical Imaging
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    note: Describes the deep learning framework for estimating prone-to-supine breast
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    pmid: null
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
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  biotoolsCURIE: biotools:hcc_segmentation_tool_for_contrast-enhanced_abdominal_ct
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  description: Features an nnU-Net based segmentation tool capable of performing HCC
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  link:
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  name: HCC segmentation tool for contrast-enhanced abdominal CT
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  biotoolsCURIE: biotools:dicom_tags_extractor
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    If a list of selected DICOM tags is provided, the tool can also produce one single
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    To use this tool, the user can download an executable file (.exe). Two execution
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    For the tool to scan data successfully, it is important that : 1/ the extension
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      3- Download the file by using the command oras pull harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_tag_extraction:1.0'
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories
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    note: null
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    note: null
    operation:
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  lastUpdate: '2025-11-04T10:59:21.506946Z'
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  link:
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  otherID: []
  owner: lsaint-aubert
  publication: []
  relation:
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    type: usedBy
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  toolType:
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  topic:
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  - term: Medical imaging
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  validated: 0
  version:
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  additionDate: '2015-06-11T13:36:38Z'
  biotoolsCURIE: biotools:metabolights
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  - note: null
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  publication:
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    metadata:
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      authors: []
      citationCount: 544
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      journal: Nucleic Acids Research
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  relation: []
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  validated: 1
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  additionDate: '2025-05-30T16:38:57.306019Z'
  biotoolsCURIE: biotools:mri_image_intensity_normalization
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  credit: []
  description: This tool enables image intensity harmonization across T2-weighted
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  documentation:
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    url: https://quibim.com/news/understanding-mri-image-harmonization/
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    note: null
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  maturity: Emerging
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  owner: xrafael
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  topic:
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  - term: Machine learning
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  - term: Medical imaging
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  validated: 0
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- accessibility: Open access
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  biotoolsCURIE: biotools:retip
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  collectionID: []
  confidence_flag: tool
  cost: Free of charge
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  description: 'Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.


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    Retip - Retention Time prediction for Metabolomics.


    Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics
    Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn
    Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.'
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  download: []
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      format:
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    - data:
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      format:
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    note: null
    operation:
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    output:
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      format:
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    - data:
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        uri: http://edamontology.org/data_0982
      format:
      - term: SMILES
        uri: http://edamontology.org/format_1196
    note: null
    operation:
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    output:
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      format:
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        uri: http://edamontology.org/format_3464
  homepage: https://www.retip.app
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  language:
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  lastUpdate: '2025-11-04T10:46:26.117809Z'
  license: CC-BY-4.0
  link:
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  - note: null
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  maturity: null
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  owner: zsmag19
  publication:
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    metadata:
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      authors: []
      citationCount: 177
      date: '2020-06-02T00:00:00Z'
      journal: Analytical Chemistry
      title: 'Retip: Retention Time Prediction for Compound Annotation in Untargeted
        Metabolomics'
    note: null
    pmcid: null
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    type: []
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  relation: []
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  topic:
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  - term: Proteomics experiment
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  - term: Machine learning
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  - term: Cheminformatics
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  - term: Chemistry
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  additionDate: '2025-10-31T09:55:55.072521Z'
  biotoolsCURIE: biotools:precision-medicine-toolbox
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  description: precision-medicine-toolbox is an open-source python package for medical
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    a tool to curate the imaging data and to perform exploratory feature analysis.
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  - note: null
    type:
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  - term: Data architecture, analysis and design
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  download:
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    - data:
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  lastUpdate: '2025-11-04T10:33:14.526964Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: recetox-xMSannotator
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    metadata: null
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    pmcid: PMC5447360
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  topic:
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  additionDate: '2025-10-29T08:08:30.731334Z'
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  confidence_flag: null
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  credit:
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    note: null
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      format:
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    note: null
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  license: GPL-2.0
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    metadata:
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  validated: 0
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  description: This tool standardizes slice thickness in CT scans by resampling them
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  license: CC-BY-NC-ND-4.0
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  name: CT Slice thickness harmonization
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  description: 'The PreciseDose system represents the first integrated computational
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    It enables organ-level prediction of drug absorption and distribution through
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    The system has been validated using external pharmacokinetic datasets and benchmarked
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    Outputs include physiologically accurate dose simulations and interactive 3D distribution
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    This record introduces a novel multidisciplinary advancement in precision pharmacology
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- accessibility: Open access
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  biotoolsCURIE: biotools:peptideshaker
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    typeEntity: Person
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  description: PeptideShaker is a search engine independent platform for interpretation
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