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18 Research products

  • Neuroinformatics
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  • LST

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
    Authors: Mühlau, Mark;

    Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimers disease.

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    bio.tools
    Software . 2019
    License: GPL-3.0
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      bio.tools
      Software . 2019
      License: GPL-3.0
      Data sources: bio.tools

  • CBGT

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools NSF | CRCNS US-German-Israeli R..., NSF | CAREER: Action Binding Du..., NSF | CRCNS: Rhythm Generation ...
    Authors: Verstynen, Timothy; Rubin, Jonathan;

    Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    bio.tools
    Software . 2019
    License: Other
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      bio.tools
      Software . 2019
      License: Other
      Data sources: bio.tools

  • THINGSvision

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python bio.tools
    Authors: Muttenthaler, Lukas; Hebart, Martin N.;

    THINGSvision is a Python toolbox for streamlining the extraction of activations from deep neural networks.

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    bio.tools
    Software . 2021
    License: MIT
    Data sources: bio.tools
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      bio.tools
      Software . 2021
      License: MIT
      Data sources: bio.tools

  • SCope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python bio.tools EC | RobustSynapses, EC | cis-CONTROL
    Authors: Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;

    SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom. This file format for very large omics datasets is maintained by the Linnarsson Lab through the loompy Python package (https://github.com/linnarsson-lab/loompy).

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    bio.tools
    Software . 2018
    License: GPL-3.0
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: GPL-3.0
      Data sources: bio.tools

  • BrainScope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018bio.tools NWO | Visual Analysis in Popula..., NWO | Genes in space
    Authors: Lew, Baldur van; Huisman, Sjoerd M. H.;

    Interactive visual exploration of the spatial and temporal human brain transcriptome.

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    bio.tools
    Software . 2018
    License: MIT
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: MIT
      Data sources: bio.tools

  • scScope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools
    Authors: Laboratory, Altschuler-Wu;

    Deep-learning based approach that can accurately and rapidly identify cell-type composition and transcriptional state from noisy single-cell gene-expression profiles containing dropout events and scale to millions of cells.

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    bio.tools
    Software . 2019
    License: Apache-2.0
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Apache-2.0
      Data sources: bio.tools

  • Geneimprint

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017bio.tools
    Authors: Jirtle, Dr Randy L.;

    Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

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    bio.tools
    Software . 2017
    Data sources: bio.tools
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      bio.tools
      Software . 2017
      Data sources: bio.tools

  • INTERPRET DSS

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java bio.tools
    Authors: group, Biomedical Applications of Magnetic Resonance research;

    Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools

  • MRICloud

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
    Authors: Oishi, Kumiko; Oishi, Kenichi;

    Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools

  • SASM-VGWAS

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
    Authors: Huang, Meiyan; Feng, Qianjin;

    Matlab package for incorporating spatial-anatomical similarity into the VGWAS framework to detect significant biomarkers in both genetic and imaging data of neurodegenerative diseases.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools
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18 Research products

  • LST

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
    Authors: Mühlau, Mark;

    Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimers disease.

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    bio.tools
    Software . 2019
    License: GPL-3.0
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: GPL-3.0
      Data sources: bio.tools

  • CBGT

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools NSF | CRCNS US-German-Israeli R..., NSF | CAREER: Action Binding Du..., NSF | CRCNS: Rhythm Generation ...
    Authors: Verstynen, Timothy; Rubin, Jonathan;

    Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways.

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    bio.tools
    Software . 2019
    License: Other
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Other
      Data sources: bio.tools

  • THINGSvision

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 Python bio.tools
    Authors: Muttenthaler, Lukas; Hebart, Martin N.;

    THINGSvision is a Python toolbox for streamlining the extraction of activations from deep neural networks.

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    bio.tools
    Software . 2021
    License: MIT
    Data sources: bio.tools
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      bio.tools
      Software . 2021
      License: MIT
      Data sources: bio.tools

  • SCope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 Python bio.tools EC | RobustSynapses, EC | cis-CONTROL
    Authors: Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;

    SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom. This file format for very large omics datasets is maintained by the Linnarsson Lab through the loompy Python package (https://github.com/linnarsson-lab/loompy).

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    bio.tools
    Software . 2018
    License: GPL-3.0
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: GPL-3.0
      Data sources: bio.tools

  • BrainScope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018bio.tools NWO | Visual Analysis in Popula..., NWO | Genes in space
    Authors: Lew, Baldur van; Huisman, Sjoerd M. H.;

    Interactive visual exploration of the spatial and temporal human brain transcriptome.

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    bio.tools
    Software . 2018
    License: MIT
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: MIT
      Data sources: bio.tools

  • scScope

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Python bio.tools
    Authors: Laboratory, Altschuler-Wu;

    Deep-learning based approach that can accurately and rapidly identify cell-type composition and transcriptional state from noisy single-cell gene-expression profiles containing dropout events and scale to millions of cells.

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    bio.tools
    Software . 2019
    License: Apache-2.0
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Apache-2.0
      Data sources: bio.tools

  • Geneimprint

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017bio.tools
    Authors: Jirtle, Dr Randy L.;

    Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

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    bio.tools
    Software . 2017
    Data sources: bio.tools
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      bio.tools
      Software . 2017
      Data sources: bio.tools

  • INTERPRET DSS

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java bio.tools
    Authors: group, Biomedical Applications of Magnetic Resonance research;

    Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools

  • MRICloud

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019bio.tools
    Authors: Oishi, Kumiko; Oishi, Kenichi;

    Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools

  • SASM-VGWAS

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    integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 MATLAB bio.tools
    Authors: Huang, Meiyan; Feng, Qianjin;

    Matlab package for incorporating spatial-anatomical similarity into the VGWAS framework to detect significant biomarkers in both genetic and imaging data of neurodegenerative diseases.

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    bio.tools
    Software . 2019
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: Unlicense
      Data sources: bio.tools
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