run_SpeckleMapping

Calculates the average speckle contrast map from Laser Speckle Contrast Imaging (LSCI) raw data.

Description

This function reads the raw speckle data stored in `speckle.dat` file and calculates the temporal average of the speckle contrast defined by the equation below:

Speckle equation

where the speckle contrast (K_s) is equal to the ratio of standard deviation (σ) to the mean intensity (I) averaged across time. The speckle contrast can be calculated either in the spatial or the temporal dimensions [1]. In brief, the estimation of the speckle contrast in space is obtained by calculating the standard deviation across a 5 by 5 pixel window which may decrease the spatial resolution. In contrast, if the calculation is performed in the temporal domain, the original spatial resolution is preserved.

Input

This function accepts image time series with dimensions Y,X,T containing LSCI data.

Output

This function creates a .dat file containing the speckle contrast map of the input data with dimensions Y,X.

Parameters

This parameter sets speckle mapping algorithm. More precisely, it chooses how the standard deviation (see description) is calculated. If set to Spatial, the standard deviation is calculated on the spatial dimension using a 5 by 5 pixel kernel. However, if set to Temporal, the function will calculate the standard deviation over the time dimension using a kernel of 5 frames.

Name of the .dat file containing the LSCI raw data. The available options are default file names from the function run_ImagesClassification function.

If true, the function will save the speckle map to a TIF file in the same folder of the input data with name std_speckle.tiff.

If true, the speckle contrast values are transformed to negative logarithm values as:

run_SpeckleMapping_eg1

References

Boas, David A., and Andrew K. Dunn. 2010. ‘Laser Speckle Contrast Imaging in Biomedical Optics’. Journal of Biomedical Optics 15 (1): 011109. https://doi.org/10.1117/1.3285504