run_HemoCompute
Calculates HbO and HbR from reflectance signals.
Description
This function uses reflectance (intrinsic) signals to estimate the concentration levels of oxygenated (HbO) and deoxygenated (HbR) hemoglobin.
Important
This function works specifically for data generated using widefield imaging systems from Labeo Technologies Inc. only!
Input
Series of .dat files containing image time series data with dimensions Y,X,T or image time series split by events with dimensions E,Y,X,T. This function uses one to three files containing reflectance (red, yellow and green) data. The file names must be the following:
- red.dat: red channel
- yellow.dat: yellow/amber channel
- green.dat: green channel
The abovementioned files are created using the run_ImagesClassification function.
Output
This function creates the files HbO.dat and HbR.dat containing the image time series with the approximate variation of the oxygenated and deoxygenated hemoglobin, respectively.
Parameters
Set of excitation and emission filters used in recordings:
- GCaMP: Filter set from recordings using GCaMP as a fluorophore
- jRGECO: Filter set from recordings using jRGECO as a fluorophore
- none: No filter set
Set this parameter to true to apply a band-pass temporal filter and normalize the data prior to the calculation of the HbR and HbO. The band-pass cut-off values are 1 and 1/120 Hz. Set to false to skip the normalization if the input data is already normalized.
If the data from the input files are already normalized (i.e. with an average around 0 or 1) and this parameter is set to true, the normalization will be skipped. However, if it is set to false and the input data is not normalized, the computation will be aborted. The normalized data is necessary for the execution of this algorithm.
If true, the function includes the Red channel in the estimation of oxy/deoxygenated hemoglobin.
If true, the function includes the Green channel in the estimation of oxy/deoxygenated hemoglobin.
If true, the function includes the Amber channel in the estimation of oxy/deoxygenated hemoglobin.