getDataFromROI

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Extracts data from ROIs.

Description

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This function extracts and aggregates data from ROIs. The function uses the ROIs stored in a ROImasks_<NAME>.mat file to extract the data from any imaging dataset created in umIT. Additionally, this function applies an aggregation function (i.e., mean, max, min, median, mode, sum or standard deviation) to summarize the pixel values from an ROI.

Input

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This function accepts any imaging data containing the dimensions Y,X as input.

Output

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The output of this function is a .mat file containing the aggregated data separated by ROI.

Note
The output of this function is used in the Analysis tab of the umIToolboxapp to visualize and compare grouped datasets.

For more information on the data structure of the output file, click here.

Parameters

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This parameter contains the name of the .mat file starting with ROImasks_ generated by the ROImanager app. This file contains the ROIs logical masks that will be used by this function to extract the ROI data.

This parameter states the function that will be used to aggregate the ROI data. The selected function will be applied to all pixels inside the ROI. Thus, this operation will reshape the input data by removing the X and Y dimensions. For instance, if the input data has dimensions Y, X and T, the output data will have dimension 1 x T.

Note
Select none extract the ROI data without aggregation. Here, the output data will still be reshaped but with dimensions N x T where N corresponds to the number of pixels inside the ROI.

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