Calculate Speckle Contrast

MATLAB functions for calculating spatial and temporal speckle contrast for performing laser speckle contrast imaging. Code developed for the Functional Optical Imaging Laboratory (FOIL) at the University of Texas at Austin.

• spatial_speckle_contrast(raw,w) - Calculate spatial speckle contrast
• temporal_speckle_contrast(raw,w) - Calculate temporal speckle contrast

Inputs

• raw - Raw data in the form of an MxNxn matrix where MxN is the dimension of a single raw image and n is the number of raw images to be processed. Note: Processing large quantities of images may require splitting the data into batches to avoid memory issues.
• w - Size of the sliding window (wxw) used during spatial speckle contrast calculation or the number of raw frames (w) used during temporal speckle contrast calcuation.

Optional Arguments (Name-Value Pairs)

• (___,'mode','gpu') - Enable GPU processing on compatible hardware. Defaults to CPU processing ('cpu').
• (___,'debug',true) - Enable verbose diagnostic information about the processing. Disabled by default (false).

Output

• sc - Matrix containing the calculated speckle contrast.
  • The output of spatial_speckle_contrast will be an MxNxn matrix. Note: The outer w/2 edge of pixels will contain unreliable information due to padding.
  • The output of temporal_speckle_contrast will be an MxNx(n-w+1) matrix.

Benchmarking

Tested performance on PC running Windows 10 with Intel i7-9700K CPU and NVIDIA GeForce RTX 2060 GPU with 1200x1000x1000 dataset.

	w	CPU	GPU
spatial_speckle_contrast	7	39 fps	106 fps
temporal_speckle_contrast	49	8.6 fps	10 fps

Citation

Colin Sullender. Calculate Speckle Contrast. (2022) doi:10.5281/zenodo.6657812.

BibTeX

@software{sullender:10.5281/zenodo.6657812,
  author       = {Colin Sullender},
  title        = {Calculate Speckle Contrast},
  month        = jun,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v1},
  doi          = {10.5281/zenodo.6657812},
  url          = {https://doi.org/10.5281/zenodo.6657812}
}

Resources

• Functional Optical Imaging Laboratory (FOIL)
• D. Boas and A. Dunn, Laser speckle contrast imaging in biomedical optics. Journal of Biomedical Optics (2010)