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:

  rescaling_of_microscopy_data/depth_dependent_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.:

  rescaling_of_microscopy_data/error_theories_manuscrpipt.ipynb

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

  rescaling_of_microscopy_data/rescaling_comparison_bead_stacks_air.ipynb rescaling_of_microscopy_data/rescaling_comparison_bead_stacks_oil.ipynb

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