run_HemoCorrection

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Performs hemodynamic correction of the fluorescence signal.

Description

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This function removes most of the hemodynamic fluctuations from the fluorescence signal using data acquired with the LabeoTech's optical imaging systems.The function uses multi-channel recordings to measure the light absorption of the hemoglobin in order to remove it from the fluorescence channel. In brief, this function applies a pixelwise linear regression of the fluorescence signal onto the reflectance signals [1,2].

Input

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Series of .dat files containing image time series data with dimensions Y,X,T. This function uses one to three files containing reflectance (red, yellow and green) data and applies the hemodynamic correction to the file containing the fluorescence data. The file names must be the following:

• fluo.dat | fluo_475.dat: fluorescence channel
• red.dat: red channel
• yellow.dat: yellow/amber channel
• green.dat: green channel

The abovementioned files are created using the run_ImagesClassification function.

Output

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Image time series with dimension Y,X,T containing the corrected fluorescence signal.

Parameters

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If true, the function includes the Red channel in the hemodynamic correction algorithm.

If true, the function includes the Green channel in the hemodynamic correction algorithm.

If true, the function includes the Amber channel in the hemodynamic correction algorithm.

References

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1. Valley, M. T., M. G. Moore, J. Zhuang, N. Mesa, D. Castelli, D. Sullivan, M. Reimers, and J. Waters. 2020. ‘Separation of Hemodynamic Signals from GCaMP Fluorescence Measured with Wide-Field Imaging’. Journal of Neurophysiology 123 (1): 356–66. https://doi.org/10.1152/jn.00304.2019.
2. Bakker, Marleen E., Ismaël Djerourou, Samuel Belanger, Frédéric Lesage, and Matthieu P. Vanni. 2023. “Alteration of Functional Connectivity despite Preserved Cerebral Oxygenation during Acute Hypoxia.” Scientific Reports 13 (1): 13269. https://doi.org/10.1038/s41598-023-40321-3.