Digital holographic microscopy (DHM) enables the three-dimensional (3D) reconstruction of quantitative phase distributions from a defocused hologram. Traditional computational algorithms follow a sequential approach in which one first reconstructs the complex amplitude distribution and later applies focusing algorithms to provide an in-focus phase map. In this work, we have developed a synergistic computational framework to compensate for the linear tilt introduced in off-axis DHM systems and autofocus the defocused holograms by minimizing a cost function, providing in-focus reconstructed phase images without phase distortions. The proposed computational tool has been validated in defocused holograms of human red blood cells and three-dimensional images of dynamic sperm cells. more »« less
Castañeda, Raul; Trujillo, Carlos; Doblas, Ana
(, PLOS ONE)
Carretero, Luis
(Ed.)
pyDHM is an open-source Python library aimed at Digital Holographic Microscopy (DHM) applications. The pyDHM is a user-friendly library written in the robust programming language of Python that provides a set of numerical processing algorithms for reconstructing amplitude and phase images for a broad range of optical DHM configurations. The pyDHM implements phase-shifting approaches for in-line and slightly off-axis systems and enables phase compensation for telecentric and non-telecentric systems. In addition, pyDHM includes three propagation algorithms for numerical focusing complex amplitude distributions in DHM and digital holography (DH) setups. We have validated the library using numerical and experimental holograms.
Bogue-Jimenez, Brian; Trujillo, Carlos; Doblas, Ana
(, PLOS ONE)
Grulkowski, Ireneusz
(Ed.)
Quantitative phase imaging (QPI) via Digital Holographic microscopy (DHM) has been widely applied in material and biological applications. The performance of DHM technologies relies heavily on computational reconstruction methods to provide accurate phase measurements. Among the optical configuration of the imaging system in DHM, imaging systems operating in a non-telecentric regime are the most common ones. Nonetheless, the spherical wavefront introduced by the non-telecentric DHM system must be compensated to provide undistorted phase measurements. The proposed reconstruction approach is based on previous work from Kemper’s group. Here, we have reformulated the problem, reducing the number of required parameters needed for reconstructing phase images to the sensor pixel size and source wavelength. The developed computational algorithm can be divided into six main steps. In the first step, the selection of the +1-diffraction order in the hologram spectrum. The interference angle is obtained from the selected +1 order. Secondly, the curvature of the spherical wavefront distorting the sample’s phase map is estimated by analyzing the size of the selected +1 order in the hologram’s spectrum. The third and fourth steps are the spatial filtering of the +1 order and the compensation of the interference angle. The next step involves the estimation of the center of the spherical wavefront. An optional final optimization step has been included to fine-tune the estimated parameters and provide fully compensated phase images. Because the proper implementation of a framework is critical to achieve successful results, we have explicitly described the steps, including functions and toolboxes, required for reconstructing phase images without distortions. As a result, we have provided open-access codes and a user interface tool with minimum user input to reconstruct holograms recorded in a non-telecentric DHM system.
Castaneda, Raul; Trujillo, Carlos; Doblas, Ana
(, Sensors)
The conventional reconstruction method of off-axis digital holographic microscopy (DHM) relies on computational processing that involves spatial filtering of the sample spectrum and tilt compensation between the interfering waves to accurately reconstruct the phase of a biological sample. Additional computational procedures such as numerical focusing may be needed to reconstruct free-of-distortion quantitative phase images based on the optical configuration of the DHM system. Regardless of the implementation, any DHM computational processing leads to long processing times, hampering the use of DHM for video-rate renderings of dynamic biological processes. In this study, we report on a conditional generative adversarial network (cGAN) for robust and fast quantitative phase imaging in DHM. The reconstructed phase images provided by the GAN model present stable background levels, enhancing the visualization of the specimens for different experimental conditions in which the conventional approach often fails. The proposed learning-based method was trained and validated using human red blood cells recorded on an off-axis Mach–Zehnder DHM system. After proper training, the proposed GAN yields a computationally efficient method, reconstructing DHM images seven times faster than conventional computational approaches.
Obando-Vásquez, Sofía; Doblas, Ana; Trujillo, Carlos
(, Optics and Lasers in Engineering)
Digital holographic microscopy (DHM) is a cutting-edge interferometric technique to recover the complex wavefield scattered by microscopic samples from digitally recorded intensity patterns. In off-axis DHM, the challenge is digitally generating the reference wavefront replica to compensate for the tilt between the interfering waves. Current methods to estimate the reference wavefront's parameters rely on brute-force grid searches or heuristics algorithms. Whereas brute-forced searches are time-consuming and impractical for video-rate quantitative phase imaging and analysis, applying heuristics methods in holographic videos is limited since the phase background level occasionally changes between frames. A semi-heuristic phase compensation (SHPC) algorithm is proposed to address these challenges to reconstruct phase images with minimum distortion in the full field-of-view (FOV) from holograms recorded by a telecentric off-axis digital holographic microscope. The method is tested with a USAF test target, smearing red blood cells and alive human sperm. The SHPC method provides accurate phase maps as the reference brute-force method but with a 92-fold reduction in processing time. Furthermore, this method was tested for reconstructing experimental holographic videos of dynamic specimens, obtaining stable phase values and minimal differences in the background between frames. This proposed method provides state-of-the-art phase reconstructions with high accuracy and stability in holographic videos, allowing the successful XYZ tracking of single-moving sperm cells.
A convolutional autoencoder for complete phase reconstruction in Digital Holographic Microscopy is reported. After proper training, this computationally efficient method reconstructs DHM holograms accurately when compared to the traditional approaches. This learning-based method is trained and validated with experimental samples of red blood cells.
@article{osti_10476321,
place = {Country unknown/Code not available},
title = {In-focus quantitative phase imaging from defocused off-axis holograms: synergistic reconstruction framework},
url = {https://par.nsf.gov/biblio/10476321},
DOI = {10.1364/OL.506400},
abstractNote = {Digital holographic microscopy (DHM) enables the three-dimensional (3D) reconstruction of quantitative phase distributions from a defocused hologram. Traditional computational algorithms follow a sequential approach in which one first reconstructs the complex amplitude distribution and later applies focusing algorithms to provide an in-focus phase map. In this work, we have developed a synergistic computational framework to compensate for the linear tilt introduced in off-axis DHM systems and autofocus the defocused holograms by minimizing a cost function, providing in-focus reconstructed phase images without phase distortions. The proposed computational tool has been validated in defocused holograms of human red blood cells and three-dimensional images of dynamic sperm cells.},
journal = {Optics Letters},
volume = {48},
number = {23},
publisher = {Optical Society of America},
author = {Castaneda, Raul and Trujillo, Carlos and Doblas, Ana},
}
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