Carlos Trujillo

Automatic method for focusing biological specimens in digital lensless holographic microscopy

A self-focusing method applicable to digital lensless holographic microscopy is presented. The method searches for the global minimum of the area enclosing a given amount of energy in a region surrounding the object of interest. The proposed modified enclosed energy method has been tested on self-focusing experimental holograms of a paramecium specimen and a section of the head of a drosophila melanogaster fly. The presented self-focusing technique also has been contrasted with some of the already reported methods to seek the best focus image.

Accelerated Numerical Processing of Electronically Recorded Holograms With Reduced Speckle Noise

The numerical reconstruction of digitally recorded holograms suffers from speckle noise. An accelerated method that uses general-purpose computing in graphics processing units to reduce that noise is shown. The proposed methodology utilizes parallelized algorithms to record, reconstruct, and superimpose multiple uncorrelated holograms of a static scene. For the best tradeoff between reduction of the speckle noise and processing time, the method records, reconstructs, and superimposes six holograms of 1024 × 1024 pixels in 68 ms; for this case, the methodology reduces the speckle noise by 58% compared with that exhibited by a single hologram. The fully parallelized method running on a commodity graphics processing unit is one order of magnitude faster than the same technique implemented on a regular CPU using its multithreading capabilities. Experimental results are shown to validate the proposal.

Automatic full compensation of quantitative phase imaging in off-axis digital holographic microscopy

An automatic method that fully compensates the quantitative phase measurements in off-axis digital holographic microscopy (DHM) is presented. The two main perturbations of the quantitative phase measurements in off-axis DHM are automatically removed. While the curvature phase flaw introduced by the microscope objective is avoided by the use of an optimized telecentric imaging system for the recording of the holograms, the remaining phase perturbation due to the tilt of the reference wave is removed by the automatic computation of a digital compensating reference wave. The method has been tested on both nonbiological and biological samples with and improving on the quality of the recovered phase maps.

Comparative analysis of the modified enclosed energy metric for self-focusing holograms from digital lensless holographic microscopy.

A comparative analysis of the performance of the modified enclosed energy (MEE) method for self-focusing holograms recorded with digital lensless holographic microscopy is presented. Notwithstanding the MEE analysis previously published, no extended analysis of its performance has been reported. We have tested the MEE in terms of the minimum axial distance allowed between the set of reconstructed holograms to search for the focal plane and the elapsed time to obtain the focused image. These parameters have been compared with those for some of the already reported methods in the literature. The MEE achieves better results in terms of self-focusing quality but at a higher computational cost. Despite its longer processing time, the method remains within a time frame to be technologically attractive. Modeled and experimental holograms have been utilized in this work to perform the comparative study.

Real-time numerical reconstruction of digitally recorded holograms

The numerical reconstruction of digitally recorded holograms has constituted the bottle neck for real-time digital holography. The reconstruction process can be understood as the diffraction that undergoes a wavefront as it illuminates the digitally recorded hologram. As this process is done numerically, the reconstruction of a M × N pixels hologram into an image of similar dimensions is an operation with a Ο (M × N)2 complexity. The diffraction process can be represented by a Fresnel transform or a scalable convolution of the recorded hologram. In these representations the numerical reconstruction has a complexity of Ο (M × log N)2, still quite demanding computationally if the holograms are of 2048 × 2048 pixels. In this work, the power provided by a Graphics Processing Unit (GPU) is used to accelerate the numerical reconstruction of digitally recorded holograms. The methodology is supported on the parallelization of typical Fresnel transform and scalable reconstruction algorithms. On reconstructing holograms of 2048 × 2048 pixels, the reconstruction is speeded up 20 times for the former method and 11 times for the scalable convolution. For holograms of 1024 × 1024, the accelerated reconstruction methods allow for real-time digital holography.

Real time numerical reconstruction of digitally recorded holograms in digital in-line holographic microscopy by using a graphics processing unit

The paper presents the way that colour can serve solving the problem of calibration points indexing in a camera geometrical calibration process. We propose a technique in which indexes of calibration points in a black-and-white chessboard are represented as sets of colour regions in the neighbourhood of calibration points. We provide some general rules for designing a colour calibration chessboard and provide a method of calibration image analysis. We show that this approach leads to obtaining better results than in the case of widely used methods employing information about already indexed points to compute indexes. We also report constraints concerning the technique. Nowadays we are witnessing an increasing need for camera geometrical calibration systems. They are vital for such applications as 3D modelling, 3D reconstruction, assembly control systems, etc. Wherever possible, calibration objects placed in the scene are used in a camera geometrical calibration process. This approach significantly increases accuracy of calibration results and makes the calibration data extraction process easier and universal. There are many geometrical camera calibration techniques for a known calibration scene [1]. A great number of them use as an input calibration points which are localised and indexed in the scene. In this paper we propose the technique of calibration points indexing which uses a colour chessboard. The presented technique was developed by solving problems we encountered during experiments with our earlier methods of camera calibration scene analysis [2]-[3]. In particular, the proposed technique increases the number of indexed points points in case of local lack of calibration points detection. At the beginning of the paper we present a way of designing a chessboard pattern. Then we describe a calibration point indexing method, and finally we show experimental results. A black-and-white chessboard is widely used in order to obtain sub-pixel accuracy of calibration points localisation [1]. Calibration points are defined as corners of chessboard squares. Assuming the availability of rough localisation of these points, the points can be indexed. Noting that differences in distances between neighbouring points in calibration scene images differ slightly, one of the local searching methods can be employed (e.g. [2]). Methods of this type search for a calibration point to be indexed, using a window of a certain size. The position of the window is determined by a vector representing the distance between two previously indexed points in the same row or column. However, experiments show that this approach has its disadvantages, as described below. * E-mail: A.Nowakowski@ire.pw.edu.pl Firstly, there is a danger of omitting some points during indexing in case of local lack of calibration points detection in a neighbourhood (e.g. caused by the presence of non-homogeneous light in the calibration scene). A particularly unfavourable situation is when the local lack of detection effects in the appearance of separated regions of detected calibration points. It is worth saying that such situations are likely to happen for calibration points situated near image borders. Such points are very important for the analysis of optical nonlinearities, and a lack of them can significantly influence the accuracy of distortion modelling. Secondly, such methods may give wrong results in the case of optical distortion with strong nonlinearities when getting information about the neighbouring index is not an easy task. Beside this, the methods are very sensitive to a single false localisation of a calibration point. Such a single false localisation can even result in false indexing of a big set of calibration points. To avoid the above-mentioned problems, we propose using a black-and-white chessboard which contains the coded index of a calibration point in the form of colour squares situated in the nearest neighbourhood of each point. The index of a certain calibration point is determined by colours of four nearest neighbouring squares (Fig.1). An order of squares in such foursome is important. Because the size of a colour square is determined only by the possibility of correct colour detection, the size of a colour square can be smaller than the size of a black or white square. The larger size of a black or white square is determined by the requirements of the exact localisation step which follows the indexing of calibration points [3]. In this step, edge information is extracted from a blackand-white chessboard. This edge information needs larger Artur Nowakowski, Wladyslaw Skarbek Institute of Radioelectronics, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warszawa, A.Nowakowski@ire.pw.edu.pl Received February 10, 2009; accepted March 27, 2009; published March 31, 2009 http://www.photonics.pl/PLP

Phase-shifting digital holographic microscopy by using a multi-camera setup

In this Letter, the use of two-coupled Mach-Zehnder interferometers for four π/2-phase shifting interferometry is introduced. A multi-camera arrangement using no more than beam splitters and mirrors is utilized to obtain in a single shot the needed phase-shifted interferograms in the different output channels of the setup. The simplicity of the setup makes it ideal for high-speed interferometry applications. This proposal is validated in digital holographic microscopy to visualize a biological sample of epidermal onion cells.

JDiffraction: A GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields ☆

Abstract JDiffraction, a GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields, is presented. Angular spectrum, Fresnel transform, and Fresnel–Bluestein transform are the numerical algorithms implemented in the methods and functions of the library to compute the scalar propagation of the complex wavefield. The functionality of the library is tested with the modeling of easy to forecast numerical experiments and also with the numerical reconstruction of a digitally recorded hologram. The performance of JDiffraction is contrasted with a library written for C++, showing great competitiveness in the apparently less complex environment of JAVA language. JDiffraction also includes JAVA easy-to-use methods and functions that take advantage of the computation power of the graphic processing units to accelerate the processing times of 2048×2048 pixel images up to 74 frames per second. Program summary Program title: JDiffraction Program Files doi: http://dx.doi.org/10.17632/nwrwz7mn7h.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: JAVA Nature of problem: In order to perform the numerical propagation of optical wave fields at any distance from the aperture the Fresnel–Kirchhoff diffraction integral must be calculated. The numerical implementation of this integral is very complex computationally, thus preventing any video-rate application that uses it. To surpass this problem Angular spectrum, Fresnel–Bluestein and Fresnel approaches have been implemented. Angular spectrum is used in any optical setup with small propagating distances. Fresnel is the fastest implementation for large propagation distances but without control of the resulting scaling of the propagated wavefields. Fresnel–Bluestein eliminates this latter problem with a slightly higher computational complexity. Solution method: Angular spectrum, Fresnel–Bluestein and Fresnel approaches for the numerical propagation of optical fields in the JAVA computation environment. Additional comments: Available for download from URL: http://unal-optodigital.github.io/JDiffraction/ . The API can be found here: http://unal-optodigital.github.io/JDiffraction/javadoc/index.html References: [1] P. Piedrahita-Quintero, C. Trujillo, J. Garcia-Sucerqui, JDiffracto 1.2 API, (2016). http://unaloptodigital.github.io/JDiffraction/javadoc/index.html (accessed June 7, 2016).

Cooperative execution of auto-focusing metrics in digital lensless holographic microscopy for internal-structured samples

The cooperative execution of two metrics to automatically determine the best focal plane in digital lensless holographic microscopy (DLHM) is presented. This proposal is comprised of two stages: first, a quick coarse search over the whole reconstruction range by using Duboiss metric allows the finding of a range in which the best focal plane can be found. In a second stage, the modified enclosed energy (MEE) metric is used within the found range in the former stage to finely determine the best focal plane. While this cooperative implementation keeps the proven effectiveness of the MEE in DLHM, it reduces by at least 11 times the total computational complexity of the auto-focusing method with respect to the MEE method only. This proposal has been validated experimentally with DLHM holograms of a paramecium specimen, polystyrene beads, and the section of the head of a Drosophila melanogaster fly.

Phase-shifting by means of an electronically tunable lens: quantitative phase imaging of biological specimens with digital holographic microscopy

The use of an electronically tunable lens (ETL) to produce controlled phase shifts in interferometric arrangements is shown. The performance of the ETL as a phase-shifting device is experimentally validated in phase-shifting digital holographic microscopy. Quantitative phase maps of a section of the thorax of a Drosophila melanogaster fly and of human red blood cells have been obtained using our proposal. The experimental results validate the possibility of using the ETL as a reliable phase-shifter device.