foa3d

A tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions.

https://github.com/lens-biophotonics/foa3d

Science Score: 39.0%

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  • DOI references
    Found 9 DOI reference(s) in README
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  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (7.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions.

Basic Info
  • Host: GitHub
  • Owner: lens-biophotonics
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 3.09 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created about 4 years ago · Last pushed 12 months ago
Metadata Files
Readme License Codemeta

README.md

Foa3D

Foa3D (3D Fiber Orientation Analysis) is a Python tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions acquired by two-photon scanning or light-sheet fluorescence microscopy.

Key features

  • parallel multiscale fiber enhancement and segmentation
  • efficient multiscale fiber orientation distribution functions
  • able to handle large tiled microscopy reconstructions

Documentation

Please read the documentation at this page: https://lens-biophotonics.github.io/Foa3D/

References

Sorelli, M., Costantini, I., Bocchi, L., Axer, M., Pavone, F. S., Mazzamuto, G. (2023), Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy, Scientific Reports, 13:4160. doi: 10.1038/s41598-023-30953-w

Alimi, A., Deslauriers-Gauthier, S., Matuschke, F., Müller, A., Muenzing, S., Axer, M., & Deriche, R. (2020). Analytical and fast fiber orientation distribution reconstruction in 3D-Polarized Light Imaging. Medical Image Analysis, 65:101760. doi: 10.1016/j.media.2020.101760

Frangi, A. F., Niessen, W. J., Vincken, K. L., & Viergever, M. A. (1998). Multiscale vessel enhancement filtering. Medical Image Computing and Computer-Assisted Intervention - MICCAI'98. 1496, pp. 130-137. Springer, Berlin, Heidelberg. doi: 10.1007/BFb0056195

Acknowledgements

The research leading to the development of this open source software was conducted within the Human Brain Project, and received funding from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the grant agreement No. 654148 (Laserlab-Europe) and the Specific Grant Agreements No. 785907 and No. 945539 (SGA2 and SGA3); from the General Hospital Corporation Center of the National Institutes of Health under the award number U01 MH117023; from the Italian Ministry for Education within the framework of the Euro-Bioimaging Italian Node (ESFRI research infrastructure); and from Fondazione CR Firenze (private foundation, project title: Human Brain Optical Mapping).

Owner

  • Name: lens-biophotonics
  • Login: lens-biophotonics
  • Kind: organization

Biophotonics group @ LENS and CNR - INO

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "3D Microscopy",
  "author": [
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  "contributor": [
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      "type": "Person",
      "affiliation": {
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        "name": "European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy; Department of Information Engineering, University of Florence, Florence, Italy"
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      "email": "sorelli@lens.unifi.it",
      "familyName": "Sorelli",
      "givenName": "Michele"
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      "id": "https://orcid.org/0000-0003-3077-3904",
      "type": "Person",
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        "type": "Organization",
        "name": "European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy; National Research Council  National Institute of Optics (CNR-INO), Sesto Fiorentino, Italy; dDepartment of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy"
      },
      "email": "mazzamuto@lens.unifi.it",
      "familyName": "Mazzamuto",
      "givenName": "Giacomo"
    }
  ],
  "dateModified": "2025-02-10",
  "description": "Foa3D (3D Fiber Orientation Analysis) is a Python tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric images acquired by two-photon scanning or light-sheet fluorescence microscopy.",
  "downloadUrl": "https://github.com/lens-biophotonics/Foa3D/archive/refs/tags/v0.1.0.zip",
  "identifier": "34f53a74-50f0-49df-a437-043a4dbc5c5b",
  "keywords": [
    "3D fluorescence microscopy",
    "connectomics",
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  "name": "Foa3D",
  "operatingSystem": [
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  "programmingLanguage": "Python 3",
  "schema:releaseNotes": "Initial release.",
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  "softwareRequirements": "Python  3.8",
  "version": "0.1.0",
  "referencePublication": "https://doi.org/10.1038/s41598-023-30953-w"
}

GitHub Events

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  • Create event: 3
  • Release event: 1
  • Issues event: 2
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  • Member event: 1
  • Push event: 60
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Delete event: 2
  • Issue comment event: 1
  • Member event: 1
  • Push event: 60

Dependencies

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