Syntax:

cellList2 = peakfinder(cellList,[cnd_new],[cnd_old],[range],[mindistold],[smooth],[signalfield],[spotsfield],[mindistnew])

cellList2 = peakfinder(cellList,...,'plot')

This function detects peaks using a signal profile, an alternative to SpotFinder. All parameters except for <cellList> are optional. The optional numeric parameters must follow the order; to use the default value of a particular parameter but still to provide the value of the following one, supply [] (empty array) for its value. All detected peaks are saved as spots in SpotFinder format with zero background, width, height, and magnitude.

• <cellList> is an array that contains the meshes. You can drag and drop the file with the data into MATLAB workspace or open it using MATLAB Import Tool. The default name of the variable is cellList, but it can be renamed.

• <cellList2> - output array of meshes.

• <cnd_new> - condition to detect a spot where no spots are present. Default: 0.25.

• <cnd_old> - condition to detect a spots where a spot already exists. Default: equal to <cnd_new>.

• <range> - range of comparison area, i.e. the number of cell segments before and after the potential peak that are taken into consideration. Default: 20.

• <mindistold> - minimum distance from the peaks existing before running peakfinder and the newly detected peaks so that they are considered identical. In such case the old peak is kept with all its properties. Default: 4.

<smooth> - degree of smoothing, number of smoothing cycles. Default: 10.

• <signalfield> - the signal field which will be processed. Must be in single quotes and must start from the word 'signal'. Default: 'signal1'.

• <spotsfield> - the spots field to which the data will be saved. Must be in single quotes and must start from the word 'spots'. Default: 'spots'.

• <mindistnew> - minimum distance separating the peaks so that they are considered distinct. Default: 0 (all peaks are distinct).

• 'plot' - display the graph and spot information for each cell as the processing goes in order to test the parameters. When the figure is displayed, press 'Enter' to continue or 'Escape' to exit.

• 'diagram' - display a diagram of the number of spots vs. cell length for quality control.