run_HemoCorrection

Performs hemodynamic correction of the fluorescence signal.

Description

This function removes most of the hemodynamic fluctuations from the fluorescence signal.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 offers two methods to perform the separation of the hemodynamic signals from the fluorescence ones:

Pixelwise linear regression [1,2]
Ratiometric [3]

Input

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 can be the following:

fluo.dat | fluo_475.dat: fluorescence channel
red.dat: red channel
yellow.dat: yellow/amber channel
green.dat: green channel
Other: other file name (only useable for the Ratiometric algorithm for now!)

The abovementioned files are created using one of the availabel Data Import functions (run_ImagesClassification or importFromTif)

Output

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

Parameters

Algorithm to be used to separate hemodynamic signals from the fluorescence channel (see references for details).

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.

Other channel to be used to remove the hemodynamic signals from the fluorescence one. Note that this option is only available for the Ratiometric algorithm for now. Please, ensure to type the file name with the extension ".dat".

References

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.
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.
Wekselblatt, Joseph B., Erik D. Flister, Denise M. Piscopo, and Cristopher M. Niell. 2016. “Large-Scale Imaging of Cortical Dynamics during Sensory Perception and Behavior.” Journal of Neurophysiology 115 (6): 2852–66. https://doi.org/10.1152/jn.01056.2015.