macro 'AutoTrack LG3-AG5';
var
  x,y,k,m,pid,h,w,a,b,e,t,q,offset,i,PicSize,HdrSize,width,height:integer;
  r:real;
begin
  HdrSize:= 0;
  h:=GetNumber('Enter height.',480);
  w:=GetNumber('Enter width.',640);
  a:=GetNumber('Frames to Average.',2);
  b:=GetNumber('Acquisition Frequency.',1);
  r:=GetNumber('Enter Frame Capture Rate (fps)',12);
  width:= w;
  height:=h;
  PicSize:=width*height;
  offset:=HdrSize;
  SetImport('8-bit');
  SetNewSize(width,height);
  MakeNewStack('AVGstack');
  e:=0;
     offset:=e*PicSize+768;
     SetCustom(width,height,offset,a);
     Import('');
    AverageSlices;
    SelectWindow('Average');
    SelectAll;
    Copy;
    Dispose;
    Dispose;
    SelectWindow('AVGstack');
    Paste;
    e:=e+b;
   for I:=1 to 20 do begin  {Macro will terminate at eof}
     offset:=e*PicSize+768;
     SetCustom(width,height,offset,a);
     Import('');
    AverageSlices;
    SelectWindow('Average');
    SelectAll;
    Copy;
    Dispose;
    Dispose;
    SelectWindow('AVGstack');
    AddSlice;
    Paste;
    e:=e+b;
  end;
   q:=GetNumber('Threshold 1-254)',170);
 for i:= 1 to nSlices do begin
    SelectSlice(i);
    invert;
   SubtractBackground('2D Rolling Ball(faster)',50);
   EnhanceContrast;
   ApplyLut;
   SetThreshold(q);
   MakeBinary;
   Erode;
   Erode;
  end;
  MakeNewWindow('TRACKSET');
  NextWindow;
  m:=nSlices;
  k:=m-1;
  for i:= 2 to k do begin
    SelectSlice(i);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    SetOption;
    DoReplace;
    NextWindow;
  end;
    NextWindow;
    MultiplybyConstant(0.5);
    NextWindow;
    SelectSlice(1);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    Add;
    MultiplybyConstant(0.75);
    NextWindow;
    SelectSlice(m);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    Add;
    rMinor[1]:=1200*b/r;
end;

macro 'TrackLength LG3-AG5';
var
  a,b,i,:integer;
  TotalLength,c,d,e,f,t,s:real;
begin
   SelectWindow('TRACKSET');
   Duplicate('TRACKSET-labeled');
   SelectWindow('TRACKSET-labeled');
   SetThreshold(1);
   MakeBinary;
   SelectWindow('AvgStack');
   SelectSlice(1);
   SelectAll;
   Copy;
   SelectWindow('TRACKSET-labeled');
   Paste;
   Subtract;
   SetThreshold(254);
   MakeBinary;
   SetOptions('Area,Length');
   IgnoreParticlesTouchingEdge(true);
   LabelParticles(true);
   SetMajorLabel('Speed u/s');
  a:=GetNumber('Enter min size.',40);
  b:=GetNumber('Enter max size.',4000);
  t:=GetNumber('Enter time in sixtieth sec.',rMinor[1]);
  s:=GetNumber('pixels/unit?',8.3);
  SetScale(s,'µm');
   SetParticleSize(a,b);
   AnalyzeParticles;
   for i:=1 to rCount do begin
   TotalLength:=0;
   c:=(rLength[i]*rLength[i])-(16*rArea[i]);
   e:=abs(c);
   d:=sqrt(e);
   TotalLength:=(rLength[i]+d)*15/t;
   rMajor[i]:=TotalLength;
   ShowResults;
   end;
end;

macro '(-' begin end;

macro 'Average LG3-AG5 Movie';
{
Imports and averages a TIFF Stack with an arbitrary number slices.
}
var
  h,w,a,b,e,offset,i,PicSize,HdrSize,width,height:integer;
  r:real;
begin
  HdrSize:= 0;
  h:=GetNumber('Enter height.',480);
  w:=GetNumber('Enter width.',640);
  a:=GetNumber('Frames to Average.',2);
  b:=GetNumber('Acquisition Frequency.',1);
  r:=GetNumber('Enter Frame Capture Rate (fps)',12);
  width:= w;
  height:=h;
  PicSize:=width*height;
  offset:=HdrSize;
  SetImport('8-bit');
  SetNewSize(width,height);
  MakeNewStack('AVGstack');
  e:=0;
     offset:=e*PicSize+768;
     SetCustom(width,height,offset,a);
     Import('');
    AverageSlices;
    SelectWindow('Average');
    SelectAll;
    Copy;
    Dispose;
    Dispose;
    SelectWindow('AVGstack');
    Paste;
    e:=e+b;
   for I:=1 to 20 do begin  {Macro will terminate at eof}
     offset:=e*PicSize+768;
     SetCustom(width,height,offset,a);
     Import('');
    AverageSlices;
    SelectWindow('Average');
    SelectAll;
    Copy;
    Dispose;
    Dispose;
    SelectWindow('AVGstack');
    AddSlice;
    Paste;
    e:=e+b;
  end;
    rMinor[1]:=1200*b/r;
end;

macro 'InvertStack';
var
  i:integer;
begin
  for i:= 1 to nSlices do begin
    SelectSlice(i);
   invert;
  end;
end;

macro 'SubtractBackground';
var
  i:integer;
begin
  for i:= 1 to nSlices do begin
    SelectSlice(i);
   SubtractBackground('2D Rolling Ball(faster)',50);
  end;
end;

macro 'EnhanceContrastStack';
var
  i:integer;
begin
  for i:= 1 to nSlices do begin
    SelectSlice(i);
   EnhanceContrast;
   ApplyLut;
  end;
end;

macro 'ThresholdStack';
var
  i:integer;
  t:integer;
begin
  t:=GetNumber('Enter Threshold Value.',170);
  for i:= 1 to nSlices do begin
    SelectSlice(i);
   SetThreshold(t);
   MakeBinary;
  end;
end;

macro 'ErodeStack';
var
  i:integer;
begin
  for i:= 1 to nSlices do begin
    SelectSlice(i);
   Erode;
  end;
end;

macro 'Track';
var
  i:integer;
  k:integer;
  m:integer;
  width:integer;
  height:integer;
begin
  GetPicSize(width,height);
  SetNewSize(width,height);
  MakeNewWindow('TRACKSET');
  NextWindow;
  m:=nSlices;
  k:=m-1;
  for i:= 2 to k do begin
    SelectSlice(i);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    SetOption;
    DoReplace;
    NextWindow;
  end;
    NextWindow;
    MultiplybyConstant(0.5);
    NextWindow;
    SelectSlice(1);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    Add;
    MultiplybyConstant(0.75);
    NextWindow;
    SelectSlice(m);
    SelectAll;
    Copy;
    NextWindow;
    Paste;
    Add;
end;

macro 'TrackLength LG3-AG5';
var
  a,b,i,:integer;
  TotalLength,c,d,e,f,t,s:real;
begin
   SelectWindow('TRACKSET');
   Duplicate('TRACKSET-labeled');
   SelectWindow('TRACKSET-labeled');
   SetThreshold(1);
   MakeBinary;
   SelectWindow('AvgStack');
   SelectSlice(1);
   SelectAll;
   Copy;
   SelectWindow('TRACKSET-labeled');
   Paste;
   Subtract;
   SetThreshold(254);
   MakeBinary;
   SetOptions('Area,Length');
   IgnoreParticlesTouchingEdge(true);
   LabelParticles(true);
   SetMajorLabel('Speed u/s');
  a:=GetNumber('Enter min size.',40);
  b:=GetNumber('Enter max size.',4000);
  t:=GetNumber('Enter time in sixtieth sec.',rMinor[1]);
  s:=GetNumber('pixels/unit?',8.3);
  SetScale(s,'µm');
   SetParticleSize(a,b);
   AnalyzeParticles;
   for i:=1 to rCount do begin
   TotalLength:=0;
   c:=(rLength[i]*rLength[i])-(16*rArea[i]);
   e:=abs(c);
   d:=sqrt(e);
   TotalLength:=(rLength[i]+d)*15/t;
   rMajor[i]:=TotalLength;
   ShowResults;
   end;
end;

macro '(-' begin end;

{FilamentLength measures the length of individual filaments.}

macro 'FilamentLength';
var
  a,b,i:integer;
  TotalLength, c,d,e,s:real;
begin
   SetThreshold(1);
   MakeBinary;
   SetOptions('Area,Length');
   IgnoreParticlesTouchingEdge(true);
   LabelParticles(true);
   SetMajorLabel('FilamentLength');
  a:=GetNumber('Enter min size.',40);
  b:=GetNumber('Enter max size.',4000);
  s:=GetNumber('pixels/unit?',8.3);
  SetScale(s,'µm');
   SetParticleSize(a,b);
   AnalyzeParticles;
   for i:=1 to rCount do begin
   TotalLength:=0;
   c:=(rLength[i]*rLength[i])-(16*rArea[i]);
   e:=abs(c);
   d:=sqrt(e);
   TotalLength:=(rLength[i]+d)/4;
   rMajor[i]:=TotalLength;
   ShowResults;
   end;
end;