openmicroscopy/bioformats

SVSReader r = new SVSReader();
r.setId("/path/to/myfile.svs");

int pixelType = r.getPixelType();
boolean floatingPoint = (pixelType == FormatTools.FLOAT || pixelType == FormatTools.DOUBLE);
int bytesPerPixel = FormatTools.getBytesPerPixel(pixelType);
boolean litteEndian = r.isLittleEndian();

for (int s=0; s<r.getSeriesCount(); s++) {
  r.setSeries(s);
  int width = r.getSizeX();
  int height = r.getSizeY();
  int z = r.getSizeZ();
  int timePoints = r.getSizeT();
  int channels = r.getSizeC();
  for (int i=0; i<r.getImageCount(); i++) {
    byte[] plane = r.openBytes(i);
    Object pixelData = DataTools.makeDataArray2D(plane, bytesPerPixel, floatingPoint, litteEndian, height);
    byte[][] pixels = (byte[][]) pixelData;
    for (int c =0; c < channels; c++) {
      for (int x =0; x < width; x++) {
        for (int y =0; y < height; y++) {
          System.out.println("Pixel Value at channel:" + c +" coordinates x: " + x + " y: " + y + " is: " + pixels[(c*x)+x][y]);
        }
      }
    }
  }
}
r.close();