{
Cell counting example. Uses the compiled peak finding routine in User.p.
The "Count Cells" macro is optimized for the included "Sample Image"
example. The macro will probably need to be customized for other images.
Parameters that may need to be changed include 'radius', 'BallRadius',
'threshold', and 'BallRadius'.
}

var {Global variable, initially zero}
  Threshold:integer; {range: 10-150}

procedure DoGammaTransform(gamma:real);
var
  i,v:integer;
  n,mode,min,max:integer
  mean:real;
begin
  measure;
  GetResults(n,mean,mode,min,max);
  ShowMessage('min=',min:1,'\max=',max:1);
  for i:=1 to 254 DO begin
    if (i>min) and (i<max)
      then v:=exp(gamma*ln((i-min)/(max-min)))*255 {x^y=exp(y*ln(x)}
      else begin
        if i<=min then v:=0 else v:=255;
      end;
    RedLUT[i]:=255-v;
    GreenLUT[i]:=255-v;
    BlueLUT[i]:=255-v;
  end;
  UpdateLUT;
end.


procedure CountCells(MoreSensative:boolean);
var
  gamma: real;
  radius: real; {peak radius; range: 1-50}
  slope: real;  {peak slope (aka peakedness); range: 0.05-0.95}
  BallRadius: real; {2d rolling ball radius}
  i,width,height: integer;
begin
  SetforegroundColor(0);
  SetbackgroundColor(255);
  radius:=6;
  slope:=0.2;
  gamma:=1.6;
  BallRadius:=8;
  {radius:=GetNumber('Radius[1-50]:',radius);}
  {slope:=GetNumber('Slope[0.05-0.95]:',slope);}
  Invert;
  SubtractBackground('2D Rolling Ball(faster)',BallRadius);
  GetPicSize(width,height);
  MakeRoi(0.05*width,0.05*height,0.9*width,0.9*height);
  EnhanceContrast;
  KillRoi;
  ApplyLUT;
  DoGammaTransform(gamma);
  ApplyLUT;
  SetOption; Smooth;
  SetOption; Smooth;
  if threshold=0 then begin
    AutoThreshold;
    wait(2);
    i:=0;
    Repeat
      i:=i+1;
    until RedLUT[i]<255;
    if MoreSensative
      then Threshold:=round(0.75*i)
      else Threshold:=i
  end;
  SetThreshold(-1);
  SetLineWidth(2);
  UserCode('Find Peaks', threshold, radius, slope);
end;


macro 'Count Cells [C]';
begin
  Threshold:=0;
  CountCells(false);
end;


macro '(-' begin end;


macro 'Count Cells-2'
begin
  Threshold:=0;
  CountCells(true);
end;


macro 'Count Cells-3'
begin
  threshold:=GetNumber('Threshold(0-255):',threshold);
  if threshold<0 then threshold:=0;
  if threshold>255 then threshold:=255;
  CountCells(false);
end;


macro 'Show Threshold';
begin
  PutMessage('Thresold=',Threshold:1);
end;