run_Ana_Speckle

Calculates the blood flow from the Laser Contrast Speckle Imaging (LSCI) data.

Description

This function uses the raw LSCI data stored in a speckle .dat file (typically speckle.dat) and calculates flow of imaged blood vessels (in arbitrary units). The algorithm used in this function is described in [1]. The input selects the execution mode: a file is read, processed and written in chunks, so the whole recording is never loaded into memory (Low-RAM mode), while an array is processed in memory (Standard mode).

Input

The raw LSCI image time series, with dimensions Y,X,T, in one of two forms:

The name (or path) of a .dat file. A bare name is looked up in the save folder. The layout is checked before processing, so a rejected file produces no output. The frame rate and the speckle exposure are read from the file header.
A numeric Y,X,T array with at least 2 frames. It carries no metadata, so FrameRateHz and ExposureMsec must be given (a pipeline provides them from the data).

Other file types and other dimension layouts are not supported.

Output

For a file input, the file Flow.dat, written in the save folder: a single-precision image time series with dimensions Y,X,T containing blood-flow values in arbitrary units. It has the same axes, sampling rate and exposure as the input file. For an array input, the single-precision Y,X,T array of blood-flow values.

Parameters

If true, the function normalizes the blood flow values of each pixel by its temporal average.

Frame rate of the input data, in Hz. It sets the width of the temporal median filter. A .dat file provides it in its header; an array needs it. If given for a file, the value overrides the header (with a warning when they differ).

Exposure time of the speckle camera, in milliseconds. It is used to convert the speckle contrast into flow. The same rules as for FrameRateHz apply.

References

Boas, David A., and Andrew K. Dunn. ‘Laser Speckle Contrast Imaging in Biomedical Optics’. Journal of Biomedical Optics 15, no. 1 (February 2010): 011109. https://doi.org/10.1117/1.3285504.