Data from: Computational 3D microscopy with optical coherence refraction tomography

• This repository contains multi-angle volumetric OCT datasets for 3D OCRT reconstruction of four biological samples (zebrafish larva, fruit fly, mouse esophagus, and mouse trachea). The OCT volumes were captured using a custom spectral domain OCT system with a parabolic mirror in the sample arm, which facilitated multi-view capture over an ultra-wide angular range. For more details, see our accompanying publication, "Computational 3D microscopy with optical coherence refraction tomography" (https://doi.org/10.1364/OPTICA.454860). We have also included TensorFlow model checkpoint files that store the system precalibration parameters for each sample. These files are utilized in the accompanying 3D reconstruction python code, which can be found here https://github.com/kevinczhou/3d-ocrt. Please visit this link for further usage instructions. ... [Read More]

Total Size

20 files (459 GB)

Data Citation

• Zhou, K., McNabb, R., Qian, R., Degan, S., Dhalla, A., Farsiu, S., & Izatt, J. (2022). Data from: Computational 3D microscopy with optical coherence refraction tomography. Duke Research Data Repository. https://doi.org/10.7924/r46h4pk10

Creator

• Degan, Simone
• Izatt, Joseph A.
• Zhou, Kevin C.
• Dhalla, Al-Hafeez
• Farsiu, Sina
• McNabb, Ryan P.
• Qian, Ruobing

DOI

• 10.7924/r46h4pk10

Subject

• Computational imaging
• Computational microscopy
• Optical coherence tomography
• 3D microscopy
• Optical coherence refraction tomography

Publication Date

• April 12, 2022

ARK

• ark:/87924/r46h4pk10

Affiliation

• Ophthalmology
• Radiology
• Biomedical Engineering

Publisher

• Duke Research Data Repository

Type

• Dataset

Format

• hdf5

Related Materials

• Kevin C. Zhou, Ryan P. McNabb, Ruobing Qian, Simone Degan, Al-Hafeez Dhalla, Sina Farsiu, and Joseph A. Izatt, "Computational 3D microscopy with optical coherence refraction tomography," Optica 9, 593-601 (2022);  https://doi.org/10.1364/OPTICA.454860
• Github repo:  https://github.com/kevinczhou/3d-ocrt

Contact

• Kevin C. Zhou, https://orcid.org/0000-0002-0351-8812, kevin.zhou@duke.edu

License

• Creative Commons CC0 1.0 Universal

Title

• Data from: Computational 3D microscopy with optical coherence refraction tomography

License

• http://creativecommons.org/publicdomain/zero/1.0/

Repository

• Duke Research Data Repository

Thumbnail	Title	Date Uploaded		Actions
	Esophagus	2022-04-12	Public
	Zebrafish	2022-04-12	Public
	Fruitfly	2022-04-12	Public
	Trachea	2022-04-12	Public