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4D Embryonic Heart

This MATLAB script is designed to synchronize 4D OCT scans of the beating heart using the TDCG method in the paper, Open-source, highly efficient, post-acquisition synchronization for 4D dual-contrast imaging of mouse embryonic heart over development with optical coherence tomography.

Dependencies

Developed for MATLAB version R2022a.

Required packages:

  • Image Processing Toolbox
  • Signal Processing Toolbox

I/O file layout

This script takes in scans in the RAW format, specified as a flat uint8 array of XYZ intensity data. The XY plane corresponds to individual B-scans, while the Z axis is the slow scanning axis. Offsets may be specified to account for file headers. Each RAW file must contain a single input channel.

Outputs:

  • "<name>/"
    • The output directory where all the TIFF files are copied to. Each image is labeled with its phase, Z position, and channel ID.
  • "imageIndices_<name>.mat"
    • a MATLAB matrix file containing the aligned image indices corresponding to each phase and Z position.
  • "<name>_log.txt"
    • A copy of all terminal outputs, when logging is enabled (verbosity >= 1).
  • "<name>_figures/"
    • The diagnostic figures as PNG and MATLAB .fig files when figure logging is enabled (verbosity >= 1).
  • "<name>.ims"
    • The TIFFs compiled as an Imaris file when the Imaris Convert path is provided.

Example usage

A simple example.

TDCG_sync({'structure.raw'}, ... % A single RAW file channel input.
  'aligned_output', ... % Save TIFF files to this directory.
	45, ... % The anticipated heart period in number of B-scans.
	[1 1 1000/20000], ... % Image scan scale in microns/pixel.
	[1024 600], ... % [height width] of B-scan (pixels).
	1:20000 ... % The subset of B-scans to use, typically all of them.
);

See alignment_example_multi.m for a more complex example processing multiple datasets, and alignment_example_with_dataset.m for a plug-and-play example using a downloadable dataset hosted on figshare.

License

See the LICENSE for more information.

Contact

Please reach out to Andre Faubert (afaubert@stevens.edu) with any questions or comments.

Acknowledgements

Funded by the National Institutes of Health (R01HD096335, R35GM142953).

A special thanks to our colleages at Dr. Shang Wang's Biophotonic's Lab!