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sf

Depth-dependent axial rescaling of 3D fluorescence microscopy data sets

https://github.com/hoogenboom-group/sf

Science Score: 57.0%

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    Found 4 DOI reference(s) in README
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    Low similarity (3.1%) to scientific vocabulary
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Repository

Depth-dependent axial rescaling of 3D fluorescence microscopy data sets

Basic Info
  • Host: GitHub
  • Owner: hoogenboom-group
  • License: cc-by-4.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 7.81 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Depth-dependent re-scaling factor

Software supporting "Depth-dependent scaling of axial distances in light microscopy" by Loginov et al. - https://doi.org/10.1364/OPTICA.520595

Created by Ernest van der Wee, Daan Boltje, Sergey Loginov

Contents

  • Online interactive tool to plot the depth-dependent axial re-scaling factor, linear theories from literature, wave-optics calculations and experimental measurements:

https://axialscaling.pythonanywhere.com/

  • Jupyter notebook to re-scale 3D microscopy data using the depth-dependent re-scaling factor:

rescalingofmicroscopydata/depthdependent_rescaling.ipynb

Data used for re-scaling was presented in "Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy" by Diel et al. - https://doi.org/10.1038/s41596-020-0360-2

We thank the authors for kindly sharing the data.

  • Plotting of Figures 9 and 12 in Loginov et al.:

rescalingofmicroscopydata/errortheories_manuscrpipt.ipynb

  • Re-scaling and plotting of Figures 10 and 13 in Loginov et al.:

rescalingofmicroscopydata/rescalingcomparisonbeadstacksair.ipynb rescalingofmicroscopydata/rescalingcomparisonbeadstacksoil.ipynb

Feedback

We are open to any comments or questions.

Owner

  • Name: hoogenboom-group
  • Login: hoogenboom-group
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.0.0
title: Re-scaling factor online plotting tool
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Ernest Benjamin
    name-particle: van der
    family-names: Wee
    email: e.b.vanderWee@tudelft.nl
    affiliation: Delft University of Technology
    orcid: 'https://orcid.org/0000-0002-0139-4019'  
  - given-names: Daan Benjamin
    family-names: Boltje
    email: d.b.boltje@tudelft.nl
    affiliation: Delft University of Technology
    orcid: 'https://orcid.org/0000-0003-4881-4700'
  - given-names: Sergey
    family-names: Loginov
    email: s.loginov@tudelft.nl
    affiliation: Delft University of Technology
version: 0.1
repository: 'https://github.com/hoogenboom-group/SF'
url: 'https://github.com/hoogenboom-group/SF'
abstract: >-
  An online interactive tool to plot the axial re-scaling 
  factor versus imaging depth and compare to depth 
  independent scaling theories.
keywords:
  - "axial scaling"
  - "optical microscope"
  - software
license: CC-BY-4.0
date-released: '2023-06-23'

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