//Stage_Movement.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 generates an micropatterned array of a desired size on the PVA-coated coverslips by photoablating the coating with an IR laser.
//To generate arrays that are larger than the microscope field of view, the macro moves the coverslip in a meander pattern. 

//Hardcoded Variables
//The provided macro creates a micoropatterned array of 5x5 fields of views located next to each other.
//These values (PatternLength, PatternHeight, StepSize) are hardcoded and should be adjusted if an array of different size is required.
//Two other input parameters required for the macro are file path of a desired pattern ablation protocol and file path of a binary map of the pattern.
//These parameters can be either hardcoded or provided through a GUI (the default option). 

int PatternLength = 5; //Length of the patterned array counted in fields of view
int PatternHeight = 5; //Height of the patterned array counted in fields of view
double StepSize = 532.48; //Microscope stage translocation between subsequent fields of view measured in micrometers

//File paths of pattern ablation protocol (line 17) and binary pattern map (line 18). 
//To hardcode the location of these files, replace the provided paths with correct ones and uncomment the commands. 
//char PatternAblationMacroPath[256] = "C:\program files\nis-elements\macros\Pattern_Stimulation.mac";
//char PatternMapPath[256] = "C:\Micropatterning\SquarePattern_100um.tif";
//Then comment or remove the entire module 'GUIs to select the ablation protocol and pattern map' (lines 23-52).

int i, j; double delta; //Temporary variables

//GUIs to select the ablation protocol and pattern map.
   char PatternAblationMacroPath[256];
   global char PatternMapPath[256];
   int returned;
   
   //By default NIS macros are saved in 'C:\Program Files\NIS-Elements\Macros\' folder.
   //Update the file path below to specify the default folder for the NIS Elements macro containing the pattern ablation protocol 
   strcpy(PatternAblationMacroPath, "C:\Program Files\NIS-Elements\Macros\");

   returned = SelectFile(PatternAblationMacroPath, "Macro for Pattern Ablation (*.mac;)|*.mac|", 0);
   if (returned==TRUE)
   {
      WaitText(0, PatternAblationMacroPath);
   }
   else
   {
      WaitText(0, "The user did not select macro for patterning");
   }

   //Path below should be updated to specify the default folder for binary maps of the micropatterns 
   strcpy(PatternMapPath, "C:\");
   returned = SelectFile(PatternMapPath, "Pattern Map (*.tif;*.tiff)|*.tif;*.tiff|", 0);
   if (returned==TRUE)
   {
      WaitText(0, PatternMapPath);
   }
   else
   {
      WaitText(0, "The user did not select pattren map");
   }

//Micropatterning routine
SetVariableValue("delta", StepSize);

for(i = 1; i <= PatternLength; i = i + 1)
   {
   if(i % 2 == 1)
      {
      for(j = 1; j <= PatternHeight; j = j +1)
         {
         if(j < PatternHeight)
            {
            RunMacro(PatternAblationMacroPath); 
            StgMoveXY(delta, 0, 1);
            }
         else
            {
            RunMacro(PatternAblationMacroPath); 
            StgMoveXY(0, delta, 1);
            }
         }
      }
   else
      {
      for(j = PatternHeight; j >= 1; j = j -1)
         {
         if(j > 1)
            {
            RunMacro(PatternAblationMacroPath); 
            StgMoveXY(-1*delta, 0, 1);
            }
         else
            {
            RunMacro(PatternAblationMacroPath); 
            StgMoveXY(0, delta, 1);
            }
         }
      }
   }