Dataset for: Quantitative phase and polarization imaging through an optical fiber applied to detection of early esophageal tumorigenesis
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Repository DOI
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Type
Dataset
Change log
Authors
Joseph, James
Alcolea, Maria P
Sawyer, Travis
Description
This folder contains data relating to the paper Gordon, G. S. D. et al. Quantitative phase and polarization imaging through an optical fiber applied to detection of early esophageal tumorigenesis. J. Biomed. Opt. 24, 1 (2019). doi: 10.1117/1.JBO.24.12.126004.
ScatteringPhantoms.zip contains raw .mat files used to produce Figure 3 (scattering phantoms)
BirefringentPhantoms.zip contains raw .mat files used to produce Figure 4 (birefringent phantoms)
MouseTissue.zip contains raw .mat files used to produce Figures 5-7 (mouse oesophagus samples)
Version
Software / Usage instructions
Scattering phantoms:
Instructions:
The file CAL/savedResults.mat contains the geometric parameters of the fibre bundle.
transferMat_L1.mat contains the full transmission matrix. The number of output pixels is 1200x1200x2 = 2880000 (the final x2 is for 2 polarisations)
Each of the Scattering folders contains data from a sample with scattering as indicated in the folder name, e.g. Scattering_0.5_1 is a sample with 0.5/mm scattering and repetition 1. Within these, the fullImage.mat contains coordinates and the recovered optical field at each of these coordinates. The other .mat files are as follows:
paramEsts.mat - recovered polarimetric parameters
polEntImage.mat - entropy images of polarisation parameters
polSigImage.mat - images of polarisation parameters but spatially averaged to match the entropy as per the paper
rawEntImage.mat - entropy of amplitude and phase
rawSigImage.mat - raw amplitude and phase images but spatially averaged to match the entropy as per the paper
The REFIM folder contains an image of sample target that validates the integrity of the transmission matrix
The CombineResults.xlsx summarises the results across the 4 samples and was used to produced figure 4.
Birefringent Phantoms instructions:
Instructions:
The file CAL/savedResults.mat contains the geometric parameters of the fibre bundle.
transferMat_L1.mat contains the full transmission matrix. The number of output pixels is 1200x1200x2 = 2880000 (the final x2 is for 2 polarisations)
Each of the Sample folders contains a repetition of the sample stretching, with different number of turns (each turn represents a ~1mm stretch)
The REFIM folder contains an image of sample target that validates the integrity of the transmission matrix
The CombineResults.xlsx summarises the results across the 4 samples and was used to produced figure 4.
Mouse tissue instructions:
Each of the sample folders contains data from a mouse esophagus sample. Samples1-6 contain lesions and Samples 7-9 are healthy controls.
The file CAL/savedResults.mat contains the geometric parameters of the fibre bundle.
transferMat_L1.mat contains the full transmission matrix. The number of output pixels is 1200x1200x2 = 2880000 (the final x2 is for 2 polarisations)
The Microscope/registeredIms.mat contains co-registered images taken from the 4 microscope imaging modalities as per the paper, as well as the masks showing healthy and lesion areas.
The SAMPLES/processed folder contains the data measured by the endoscope.
fullImage.mat - raw image - each point is a 2D complex number representing amplitude and phase in two pols
paramEsts.mat - recovered polarimetric parameters
polEntImage.mat - entropy images of polarisation parameters
polSigImage.mat - images of polarisation parameters but spatially averaged to match the entropy as per the paper
rawEntImage.mat - entropy of amplitude and phase
rawSigImage.mat - raw amplitude and phase images but spatially averaged to match the entropy as per the paper
The REFIM folder contains an image of sample target that validates the integrity of the transmission matrix
The CombineResults.xlsx summarises the results across the 4 samples and was used to produced figure 4.
Keywords
quantitative phase imaging, polarisation imaging
Publisher
Sponsorship
European Commission (630729)
Cancer Research Uk (None)
Engineering and Physical Sciences Research Council (EP/N014588/1)
Cancer Research UK (21102)
Cancer Research UK (24669)
Engineering and Physical Sciences Research Council (EP/R003599/1)
Cancer Research Uk (None)
Engineering and Physical Sciences Research Council (EP/N014588/1)
Cancer Research UK (21102)
Cancer Research UK (24669)
Engineering and Physical Sciences Research Council (EP/R003599/1)