macro 'Rotating LineScan' {
      defaultRotationRange=10;
      defaultRotationStep=1;
      defaultMeasureRange=2;
      defaultChannelPeak=1;
      defaultDisplayPeakOverlay=1;
      trackingModeAsDefault=1;
      title=getTitle();
      Stack.getPosition(channel, slice, frame);
      Stack.getDimensions(width, height, channels, slices, frames);
      if (defaultChannelPeak>channels) defaultChannelPeak=channels;
      if (selectionType()!=5) exit("trace a straight line before starting the macro");
      channelsList=newArray(channels);
      for (i=0; i<channels; i++) channelsList[i]=d2s(i+1, 0);
      showAreas=newArray("ROIs", "overlays");
      scanningModes=newArray(1, 2, 3);
      Dialog.create("Rotating linescan - options");
          Dialog.addNumber("Rotation range: "+fromCharCode(177), defaultRotationRange, 0, 1, "degrees");
          Dialog.addNumber("Rotation step:", defaultRotationStep, 2, 1, "degrees");
          Dialog.addNumber("Measure around:"+ fromCharCode(177), defaultMeasureRange, 0, 0, "pixels");
          if (channels>1) Dialog.addChoice("Find cortex on channel:", channelsList, channelsList[defaultChannelPeak-1]);
          Dialog.addCheckbox("Display positions as overlays (removes current overlays)", defaultDisplayPeakOverlay);
          Dialog.addCheckbox("Recenter and reorient the linescan at every frame", trackingModeAsDefault);
      Dialog.show();
      rotationRange=Dialog.getNumber();
      rotationRange=-rotationRange;
      rotationStep=Dialog.getNumber();
      sumNpixels=Dialog.getNumber();
      if (channels>1) channelPeak=parseInt(Dialog.getChoice());
      else channelPeak=1;
      peakOverlay=Dialog.getCheckbox();
      trackingMode=Dialog.getCheckbox();
      if (selectionType()!=5) exit("line selection required");
      getLine(x1, y1, x2, y2, lineWidth);
      setLineWidth(lineWidth);
      x3=x2-(x2-x1)/2;
      y3=y2-(y2-y1)/2;
      hypotenuse=sqrt(pow(x2-x3, 2)+pow(y2-y3, 2));
      if (x1>x2 && y1<y2) initialAngle=acos((-abs(x3-x2))/hypotenuse);
      else if (x1<x2 && y1>y2)  initialAngle=acos((-abs(x3-x2))/hypotenuse);
      else initialAngle=acos((abs(x3-x2))/hypotenuse);
      if (y1>y2) initialAngle=initialAngle+PI;
      results="";
      x4=newArray(frames);
      y4=newArray(frames);
      x5=newArray(frames);
      y5=newArray(frames);
      signal="";
      if (peakOverlay==1) Overlay.remove;
      for (t=1; t<=frames; t++) {
          Stack.setChannel(channelPeak);
          wait(50);
          Stack.setFrame(t);
          MaxPeak=newArray((-rotationRange*2*1/rotationStep)+2);
          MaxPeakPosition=newArray((-rotationRange*2*1/rotationStep)+2);
          j=0;
          for (k=rotationRange*PI/180; k<=-rotationRange*PI/180; k+=rotationStep*PI/180) {
              scanningAngle=initialAngle+k+PI;      
              X1=x3+cos(scanningAngle)*hypotenuse;
              Y1=y3+sin(scanningAngle)*hypotenuse;
              X2=x3+cos(scanningAngle+PI)*hypotenuse;
              Y2=y3+sin(scanningAngle+PI)*hypotenuse;
              makeLine(X1,Y1,X2,Y2,lineWidth);
              LineScan0=getProfile();
              LineScan=newArray(lengthOf(LineScan0));
              for (i=1; i<lengthOf(LineScan)-1; i++) LineScan[i]=LineScan0[i-1]+LineScan0[i]+LineScan0[i+1];
              Positions=Array.rankPositions(LineScan);
              Array.reverse(Positions);
              MaxPeakPosition[j]=Positions[0];
              MaxPeak[j]=LineScan[Positions[0]];
              j=j+1;
          }
          MaxPeakAngle=Array.rankPositions(MaxPeak);
          Array.reverse(MaxPeakAngle);
          MaxPeakPosition=MaxPeakPosition[MaxPeakAngle[0]];
          MaxPeakAngle=rotationRange*PI/180+MaxPeakAngle[0]*rotationStep*PI/180;
          scanningAngle=initialAngle+MaxPeakAngle+PI;
          X1=x3+cos(scanningAngle)*hypotenuse;
          Y1=y3+sin(scanningAngle)*hypotenuse;
          X2=x3+cos(scanningAngle+PI)*hypotenuse;
          Y2=y3+sin(scanningAngle+PI)*hypotenuse;
          makeLine(X1,Y1,X2,Y2,lineWidth);
          X3=X1+(X2-X1)*MaxPeakPosition/lengthOf(LineScan);
          Y3=Y1+(Y2-Y1)*MaxPeakPosition/lengthOf(LineScan);
          hypothenuse2=lineWidth/2;
          angleBox=scanningAngle+PI/2;
          x4[t-1]=X3-cos(angleBox)*hypothenuse2;
          y4[t-1]=Y3-sin(angleBox)*hypothenuse2;
          x5[t-1]=X3+cos(angleBox)*hypothenuse2;
          y5[t-1]=Y3+sin(angleBox)*hypothenuse2;
          if (trackingMode==1) {
              x3=x3+cos(scanningAngle)*(hypotenuse-MaxPeakPosition);
              y3=y3+sin(scanningAngle)*(hypotenuse-MaxPeakPosition);
              initialAngle=scanningAngle+PI;
          }
      }
      for (t=1; t<=frames; t++) {
          Stack.setFrame(t);
          if (sumNpixels==0) {
              for (c=1; c<=channels; c++) {
                  Stack.setChannel(c);
                  LineScan=getProfile();
                  signal=signal+toString(LineScan[MaxPeakPosition])+fromCharCode(9);
              }
          }
          else {
              makeLine(x4[t-1], y4[t-1], x5[t-1], y5[t-1], (sumNpixels*2)+1);
              run("Line to Area");
              for (c=1; c<=channels; c++) {
                  Stack.setChannel(c);
                  List.setMeasurements;
                  signal=signal+toString(List.getValue("Mean"))+fromCharCode(9);
              }
              if (peakOverlay==1) {
                  if (Stack.isHyperstack) {
                      makeLine(x4[t-1], y4[t-1], x5[t-1], y5[t-1]);
                      Overlay.addSelection("#4dffff00", 1);
                      Overlay.setPosition(0, slice, t);
                      makeLine(x4[t-1], y4[t-1], x5[t-1], y5[t-1]);
                      Overlay.addSelection("#4d00ffff", (sumNpixels*2)+1);
                      Overlay.setPosition(0, slice, t);
                  }
                  else {
                      makeLine(x4[t-1], y4[t-1], x5[t-1], y5[t-1]);
                      Overlay.addSelection("#4dffff00", 1);
                      Overlay.setPosition(t);
                      makeLine(x4[t-1], y4[t-1], x5[t-1], y5[t-1]);
                      Overlay.addSelection("#4d00ffff", (sumNpixels*2)+1);
                      Overlay.setPosition(t);
                  }
              }
          }
          signal=substring(signal, 0, lengthOf(signal)-1);
          signal=signal+"\n";
      }
      signal=substring(signal, 0, lengthOf(signal)-1);
      String.copy(signal);
      Stack.setPosition(channel, slice, frame);
      makeLine(x1, y1, x2, y2, lineWidth);
      showStatus("done, results copied to clipboard");
  }