Quick and dirty Euglena tracking using OpenCV, Syphon, and OSC[[OSC|Open Sound Control]].

Sources at GitHub: https://github.com/lscherff/biogames/tree/master/TrackEuglenaSyphonOSC

Threshold based Euglena detection

opencv.loadImage(cam);

opencv.gray();
opencv.invert();

opencv.erode();
opencv.dilate();

threshold = int(map(mouseX,0,width,0,255));
opencv.threshold(threshold);

// ...

contours = opencv.findContours();

Skipping large/small/malformed contours

for (Contour contour : contours) {
      float a = contour.area();
      Rectangle r = contour.getBoundingBox();
      float wh = float(r.width)/float(r.height);
      if (a > minArea && wh > 0.1 && wh < 10 && a < maxArea) {
      // ...

Maintaining Euglena identity in a list (based on proximity from frame to frame), computing speed as dx, dy and mean speed as mdx, mdy

void checkEuglena(Contour c) {
  boolean found = false;
  Rectangle r = c.getBoundingBox();
  for (Euglena e : euglenaList) {
    if (dist(e.x, e.y, r.x, r.y) < distanceThreshold) {
      e.dx = e.x - r.x;
      e.dy = e.y - r.y;
      e.x = r.x;
      e.y = r.y;
      e.found = true;
      found = true;
      break;
    }
  }
  if (!found) {
    euglenaList.add(new Euglena(r.x, r.y));
  }
}

void deleteEuglena() {
  ListIterator<Euglena> iter = euglenaList.listIterator();
  float newmdx = 0;
  float newmdy = 0;
  while (iter.hasNext()) {
    Euglena e = iter.next();
    if (e.found==false) iter.remove();
    else {
      e.found = false;
      newmdx = newmdx + e.dx;
      newmdy = newmdy + e.dy;
    }
  }
  if (euglenaList.size() > 0) {
    newmdx = newmdx / euglenaList.size();
    newmdy = newmdy / euglenaList.size();
  } else {
    newmdx = 0;
    newmdy = 0;
  }
  mdx += (newmdx - mdx)*0.01;
  mdy += (newmdy - mdy)*0.01;
}