Computational Optical Sensing and Processing Laboratory

Digital Holographic Microscopy Group

Staff

Leader: Ákos Zarándy PhD DsC
Researchers: László Orzó PhD, Szabolcs Tőkés PhD
PhD student: Márton Kiss and several BSc and MSc students
Engineers: Balázs Wittner

Contact

Research topic and mission

  • Automatic water quality monitoring
  • Volume inspection and recognition based on a morphological database
  • Color Digital Holographic Microscope
  • 200x increase in inspected volume - compared to conventional microscopy
  • Detection, recognition, classification, and counting of algae, bacteria, worms, (indicator species) etc.
  • Current setup inspects 2µl/sec of dense fluid samples, and 0.5L/h of drinking water (with pre-condensation)
  • Automatic alarm in case of environmental health hazards

By using Digital Holographic Microscopy, we are able to gather visual information from a volume and thus circumvent the small depth of field constraint of conventional microscopes. This way, a volume inspection system can be constructed, which is able to find, segment, collect, and later classify the objects that flow through an inspection chamber. Our current application is the detection, recognition, and classification of the biological content in natural fresh water and drinking water.

OpticalSetup

In an in-line digital holographic microscope the measured hologram is produced by the interference of the reference beam, which serves also for the illumination, and the light diffracted from the objects. Unlike conventional microscopy, this method provides holograms from out of focus objects, which can be reconstructed numerically, thus virtually enabling a numerical Z scan of a larger volume from a single captured image. Our setup is capable of imaging a 1 [mm3] volume with 1 [µm] resolution from a single frame. The total reconstruction process time of one frame is usually less than one second, thanks to the sophisticated GPU algorithms. The microscope with a color video camera captures and processes 2 frames per second, thus the total examined volume is 2 [µl/sec]. For larger volumes of less dense fluids, such as drinking water, a tangential flow pre-filtration system is used, which condenses the liquid by removing the excess water through a 0.45 µm membrane filter.

The second Prototype system

After capturing the raw color holograms, we use several algorithmic steps to enhance image quality. This solution includes an automatic background elimination to reduce the speckle noise and to remove the diffraction patterns of dust particles located in the optical path.

Captured hologram and the reconstructed algae

The reconstructed, segmented objects are stored in a PC for further processing with an adaptive model based classification algorithm. A sophisticated feature selection method is applied to create a database of biological microorganisms. Machine learning algorithms analyze the captured images, classifying the various algae types. Currently, the whole process of examining 1L of drinking water takes approximately 2 Hours, and needs no human intervention. Extensive R&D is in progress to enhance the system performance.

Developments

Design of the 1st Prototype System

Design of the 2nd Prototype System

Components of the DHM prototype

DHM2.0 laser pump sample holder microscope camera condenser coupler

Reconstructions

Reconstruction of an algae hologram

Reconstruction of an algae hologram

Reconstruction of an algae hologram

Infrastructure

  • Special illumination by fiber coupled three color (RGB) Lasers
  • Reconstruction softwares (speed up by GPU)
  • Flow through cell for water monitoring application
  • DHM micro-organism database
  • Microscopes, objectives
  • Optical laboratory equipments

Application - DHM for worm detection

Besides the DHM designed for the detection of algae, we have developed a prototype that is able to detect larger objects and particles (20µm-150µm) floating within the water. In this setup we apply a so called lens-less DHM setup, where the optical system includes only a camera and a coherent light source but does not apply any type of lens or microscope objective. Since the different kinds of worms are the typical objects in the above-mentioned size range, the constructed lens-less device can be applied efficiently for the detection of worms. Therefore, with our industrial partners (Knot LLC., BÁCSVÍZ Ltd.) we have developed a modified DHM, aiming especially worm detection. Since the worms usually have no typical coloration, we do not apply the special three-color light source developed for alga detection, just a single laser. Further simplification hade been applied on the fluid control, because using this setup we can monitor quite large volume (0.3 cm3) from each hologram. This way we do not need sample condensation used in the earlier DHM setups and we have to use a quite different flow through measuring chamber.

The most advanced version of the device:

We applied the worm monitoring setup successfully in pilot experiments, where the cleaning process of a test water well filter was supervised by the device real time. Using the conventional measuring methods - which can be fulfilled only infrequently; takes much longer times; and are more expensive – it is not possible to start and schedul the required cleaning process appropriately. Without real time monitoring of the progress of the cleaning process the required, fault proof procedure would takes much longer time and would results in considerable waste of water and energy. During pilot our measurement device were able to handle the above challenges successfully.

Test results show how changes the number of worms in the water samples during the different steps of the cleaning process.

Partners

Publications

  • Z. Göröcs, M. Kiss, V. Tóth, L. Orzó, and S. Tőkés. "Multicolor digital holographic microscope (dhm) for biological purposes." 7568:75681P, 2010. pdf
  • Z. Göröcs, L. Orzó, M. Kiss, V. Tóth, and S. Tőkés. "In-line color digital holographic microscope for water quality measurements." 7376:737614, 2010. pdf
  • L. Orzó, Z. Göröcs, I. Szatmári, and S. Tőkés. "Gpu implementation of volume reconstruction and object detection in digital holographic microscopy." In Cellular Nanoscale Networks and Their Applications (CNNA), 2010 12th International Workshop on, pages 1–4. IEEE, 2010. pdf
  • M.Z. Kiss, Z. Göröcs, and S. Tőkés. " Self-referenced digital holographic microscopy." In Cellular Nanoscale Networks and Their Applications (CNNA), 2012 13th International Workshop on, pages 1–4. IEEE, 2012. pdf
  • S. Tőkés and L. Orzó. "Afocal digital holographic microscopy and its advantages." In Cellular Nanoscale Networks and Their Applications (CNNA), 2012 13th International Workshop on, pages 1–5. IEEE, 2012. pdf
  • B. Nagy and S. Tőkés. "Study on application of reference conjugated hologram for aberration correction of multiple object planes." In Cellular Nanoscale Networks and Their Applications (CNNA), 2012 13th International Workshop on, pages 1–4. IEEE, 2012. pdf
  • L. Orzó, A. Fehér, and S. Tőkés. "Advanced background elimination in digital holographic microscopy." In Cellular Nanoscale Networks and Their Applications (CNNA), 2012 13th International Workshop on, pages 1–5. IEEE, 2012. pdf
  • L. Orzó, Z. Göröcs, A. Fehér, and S. Tőkés. "In-line hologram segmentation for volumetric samples. Applied Optics, 52(1):A45–A55, 2013. pdf
    This paper was published in Applied Optics and is made available as an electronic reprint with thepermission of OSA. The paper can be found at the following URL on the OSA website: 10.1364/AO.52.000A45. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law.
  • László Orzó, Balázs Wittner, and Szabolcs Tőkés. " High speed water monitoring systems based on digital holographic microscopy. " In Computer Science and Information Technologies (CSIT), 2013, pages 1–9, Sept 2013. (doi: 10.1109/CSITechnol.2013.6710366) pdf
  • M. Kiss, B. Nagy, P. Lakatos, Z. Göröcs, S. Tőkés, B. Wittner, and L. Orzó, "Special multicolor illumination and numerical tilt correction in volumetric digital holographic microscopy," Opt. Express 22, 7559-7573 (2014). pdf
  • L. Orzó, "High speed phase retrieval of in-line holograms by the assistance of corresponding off-axis holograms," Opt. Express 23(13), 16638-16649 (2015). pdf

Awards

FET'11, 3rd prize, best exhibit

Supporting grants

This project, (NKTH 1981822A), titled “Water Biology Digital Holographic Microscope (DHM) as an early warning environmental system” was funded by the Hungarian National Office for Research and Technology.