//Pattern_Stimulation.mac is a macro designed for NIS Elements (Nikon Instruments) and validated with the version 5.21.30 (Build 1489) of the software.
//This macro contains a protocol of micropattern photoablation on a multi-photon microscope powered by NIS Elements.

//Ablate a small fiduciary marker in the center of the field of view
SelectOptConf("Print_Fiduciary_Marker"); //burn a small square through many Z-planes
ND_RunZSeriesExp();

//Focus the microscope on the PVA coated surface of the coverslip
SelectOptConf("Autofocus"); //Use autofocus to find the best focal plane
StgFocus();

//Pattern the desired micropattern. File path for binary map of the pattern is stored in PatternMapPath variable.   
SelectOptConf("Load_ROI"); //capture a 2048 image to load the ROI which is also 2048
CloseAllDocuments(2);
Capture();
ClearMeasROI();
LoadROI(PatternMapPath,1);
ChangeROIType(1,3); //set the desired ROIs as stimulation ROI
ChangeROIType(2,3);
ChangeROIType(3,3);
ChangeROIType(8,3);
ChangeROIType(9,3);
ChangeROIType(12,3);
ChangeROIType(13,3);
ChangeROIType(14,3);
A1ApplyStimulationSettings(); //Apply Stimulation settings in ND stimulation
SelectOptConf("Micropattern"); //Pattern in the number of Z planes defined in the ND stimulation settings
ND_RunSequentialStimulationExp();