1
|
Valentino M, Sirico DG, Memmolo P, Miccio L, Bianco V, Ferraro P. Digital holographic approaches to the detection and characterization of microplastics in water environments. APPLIED OPTICS 2023; 62:D104-D118. [PMID: 37132775 DOI: 10.1364/ao.478700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microplastic (MP) pollution is seriously threatening the environmental health of the world, which has accelerated the development of new identification and characterization methods. Digital holography (DH) is one of the emerging tools to detect MPs in a high-throughput flow. Here, we review advances in MP screening by DH. We examine the problem from both the hardware and software viewpoints. Automatic analysis based on smart DH processing is reported by highlighting the role played by artificial intelligence for classification and regression tasks. In this framework, the continuous development and availability in recent years of field-portable holographic flow cytometers for water monitoring also is discussed.
Collapse
|
2
|
Valentino M, Bianco V, Miccio L, Memmolo P, Brancato V, Libretti P, Gambacorta M, Salvatore M, Ferraro P. Beyond conventional microscopy: Observing kidney tissues by means of fourier ptychography. Front Physiol 2023; 14:1120099. [PMID: 36860516 PMCID: PMC9968938 DOI: 10.3389/fphys.2023.1120099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Kidney microscopy is a mainstay in studying the morphological structure, physiology and pathology of kidney tissues, as histology provides important results for a reliable diagnosis. A microscopy modality providing at same time high-resolution images and a wide field of view could be very useful for analyzing the whole architecture and the functioning of the renal tissue. Recently, Fourier Ptychography (FP) has been proofed to yield images of biology samples such as tissues and in vitro cells while providing high resolution and large field of view, thus making it a unique and attractive opportunity for histopathology. Moreover, FP offers tissue imaging with high contrast assuring visualization of small desirable features, although with a stain-free mode that avoids any chemical process in histopathology. Here we report an experimental measuring campaign for creating the first comprehensive and extensive collection of images of kidney tissues captured by this FP microscope. We show that FP microscopy unlocks a new opportunity for the physicians to observe and judge renal tissue slides through the novel FP quantitative phase-contrast microscopy. Phase-contrast images of kidney tissue are analyzed by comparing them with the corresponding renal images taken under a conventional bright-field microscope both for stained and unstained tissue samples of different thicknesses. In depth discussion on the advantages and limitations of this new stain-free microscopy modality is reported, showing its usefulness over the classical light microscopy and opening a potential route for using FP in clinical practice for histopathology of kidney.
Collapse
Affiliation(s)
- Marika Valentino
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy,Department of Electric and Information Technologies Engineering, University of Naples “Federico II”, Naples, Italy
| | - Vittorio Bianco
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy,*Correspondence: Vittorio Bianco, ; Marcello Gambacorta,
| | - Lisa Miccio
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
| | - Pasquale Memmolo
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
| | | | | | - Marcello Gambacorta
- IRCCS SYNLAB SDN, Naples, Italy,*Correspondence: Vittorio Bianco, ; Marcello Gambacorta,
| | | | - Pietro Ferraro
- National Research Council (CNR) of Italy, Institute of Applied Sciences and Intelligent Systems (ISASI), Pozzuoli, Italy
| |
Collapse
|
3
|
Běhal J, Borrelli F, Mugnano M, Bianco V, Capozzoli A, Curcio C, Liseno A, Miccio L, Memmolo P, Ferraro P. Developing a Reliable Holographic Flow Cyto-Tomography Apparatus by Optimizing the Experimental Layout and Computational Processing. Cells 2022; 11:cells11162591. [PMID: 36010667 PMCID: PMC9406712 DOI: 10.3390/cells11162591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Digital Holographic Tomography (DHT) has recently been established as a means of retrieving the 3D refractive index mapping of single cells. To make DHT a viable system, it is necessary to develop a reliable and robust holographic apparatus in order that such technology can be utilized outside of specialized optics laboratories and operated in the in-flow modality. In this paper, we propose a quasi-common-path lateral-shearing holographic optical set-up to be used, for the first time, for DHT in a flow-cytometer modality. The proposed solution is able to withstand environmental vibrations that can severely affect the interference process. Furthermore, we have scaled down the system while ensuring that a full 360° rotation of the cells occurs in the field-of-view, in order to retrieve 3D phase-contrast tomograms of single cells flowing along a microfluidic channel. This was achieved by setting the camera sensor at 45° with respect to the microfluidic direction. Additional optimizations were made to the computational elements to ensure the reliable retrieval of 3D refractive index distributions by demonstrating an effective method of tomographic reconstruction, based on high-order total variation. The results were first demonstrated using realistic 3D numerical phantom cells to assess the performance of the proposed high-order total variation method in comparison with the gold-standard algorithm for tomographic reconstructions: namely, filtered back projection. Then, the proposed DHT system and the processing pipeline were experimentally validated for monocytes and mouse embryonic fibroblast NIH-3T3 cells lines. Moreover, the repeatability of these tomographic measurements was also investigated by recording the same cell multiple times and quantifying the ability to provide reliable and comparable tomographic reconstructions, as confirmed by a correlation coefficient greater than 95%. The reported results represent various steps forward in several key aspects of in-flow DHT, thus paving the way for its use in real-world applications.
Collapse
Affiliation(s)
- Jaromír Běhal
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Francesca Borrelli
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Martina Mugnano
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Vittorio Bianco
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Amedeo Capozzoli
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Claudio Curcio
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Angelo Liseno
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Lisa Miccio
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Pasquale Memmolo
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
- Correspondence:
| | - Pietro Ferraro
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| |
Collapse
|
4
|
Pirone D, Sirico D, Miccio L, Bianco V, Mugnano M, Ferraro P, Memmolo P. Speeding up reconstruction of 3D tomograms in holographic flow cytometry via deep learning. LAB ON A CHIP 2022; 22:793-804. [PMID: 35076055 DOI: 10.1039/d1lc01087e] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tomographic flow cytometry by digital holography is an emerging imaging modality capable of collecting multiple views of moving and rotating cells with the aim of recovering their refractive index distribution in 3D. Although this modality allows us to access high-resolution imaging with high-throughput, the huge amount of time-lapse holographic images to be processed (hundreds of digital holograms per cell) constitutes the actual bottleneck. This prevents the system from being suitable for lab-on-a-chip platforms in real-world applications, where fast analysis of measured data is mandatory. Here we demonstrate a significant speeding-up reconstruction of phase-contrast tomograms by introducing in the processing pipeline a multi-scale fully-convolutional context aggregation network. Although it was originally developed in the context of semantic image analysis, we demonstrate for the first time that it can be successfully adapted to a holographic lab-on-chip platform for achieving 3D tomograms through a faster computational process. We trained the network with input-output image pairs to reproduce the end-to-end holographic reconstruction process, i.e. recovering quantitative phase maps (QPMs) of single cells from their digital holograms. Then, the sequence of QPMs of the same rotating cell is used to perform the tomographic reconstruction. The proposed approach significantly reduces the computational time for retrieving tomograms, thus making them available in a few seconds instead of tens of minutes, while essentially preserving the high-content information of tomographic data. Moreover, we have accomplished a compact deep convolutional neural network parameterization that can fit into on-chip SRAM and a small memory footprint, thus demonstrating its possible exploitation to provide onboard computations for lab-on-chip devices with low processing hardware resources.
Collapse
Affiliation(s)
- Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
- DIETI, Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", via Claudio 21, 80125 Napoli, Italy
| | - Daniele Sirico
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Martina Mugnano
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| |
Collapse
|
5
|
Sirico DG, Cavalletti E, Miccio L, Bianco V, Memmolo P, Sardo A, Ferraro P. Kinematic analysis and visualization of Tetraselmis microalgae 3D motility by digital holography. APPLIED OPTICS 2022; 61:B331-B338. [PMID: 35201156 DOI: 10.1364/ao.444976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
A study on locomotion in a 3D environment of Tetraselmis microalgae by digital holographic microscopy is reported. In particular, a fast and semiautomatic criterion is revealed for tracking and analyzing the swimming path of a microalga (i.e., Tetraselmis species) in a 3D volume. Digital holography (DH) in a microscope off-axis configuration is exploited as a useful method to enable fast autofocusing and recognition of objects in the field of view, thus coupling DH with appropriate numerical algorithms. Through the proposed method we measure, simultaneously, the tri-dimensional paths followed by the flagellate microorganism and the full set of the kinematic parameters that describe the swimming behavior of the analyzed microorganisms by means of a polynomial fitting and segmentation. Furthermore, the method is capable to furnish the accurate morphology of the microorganisms at any instant of time along its 3D trajectory. This work launches a promising trend having as the main objective the combined use of DH and motility microorganism analysis as a label-free and non-invasive environmental monitoring tool, employable also for in situ measurements. Finally, we show that the locomotion can be visualized intriguingly by different modalities to furnish marine biologists with a clear 3D representation of all the parameters of the kinematic set in order to better understand the behavior of the microorganism under investigation.
Collapse
|
6
|
Cai W, Chen L, Xiao J, Li J, Hu Y, Wen K. Elimination of abnormal phase fluctuation in digital holography. APPLIED OPTICS 2022; 61:1035-1040. [PMID: 35201076 DOI: 10.1364/ao.448986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
In digital holography, the phase is most important, and the quality of the reconstructed phase determines the final reconstructed image effect. However, noise is inevitably introduced in the process of recording the hologram. For regions without object light, the phase has a random distribution, which affects the final phase quality. This kind of noise is called abnormal phase fluctuations in this paper. The correlation between amplitude and phase in digital holography is used to judge whether there is useful phase information. Through structural similarity and the light-dark relationship, a credible probability mask is introduced to extract the phase that needs to be preserved. The simulation and experimental results show that abnormal phase fluctuations are successfully removed, and the useful phase information is retained.
Collapse
|
7
|
Montresor S, Tahon M, Picart P. Deep learning speckle de-noising algorithms for coherent metrology: a review and a phase-shifted iterative scheme [Invited]. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:A62-A78. [PMID: 35200959 DOI: 10.1364/josaa.444951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We present a review of deep learning algorithms dedicated to the processing of speckle noise in coherent imaging. We focus on methods that specifically process de-noising of input images. Four main classes of applications are described in this review: optical coherence tomography, synthetic aperture radar imaging, digital holography amplitude imaging, and fringe pattern analysis. We then present deep learning approaches recently developed in our group that rely on the retraining of residual convolutional neural network structures to process decorrelation phase noise. The paper ends with the presentation of a new approach that uses an iterative scheme controlled by an input SNR estimator associated with a phase-shifting procedure.
Collapse
|
8
|
Biospeckle Analysis and Biofilm Electrostatic Tests, Two Useful Methods in Microbiology. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of more sensitive methodologies, capable of quickly detecting and monitoring a microbial population present in a specific biological matrix, as well as performing to allow for the study of all its metabolic changes (e.g., during the formation of biofilm) to occur, is an essential requirement for both well-being and the food industry. Two techniques, in particular, have gained the attention of scientists: The first is “biospeckle”, an optical technique representing an innovative tool for applications in food quality, food safety, and nutraceuticals. With this technique, we can quickly evaluate and monitor the presence of bacteria (or their proliferation) in a solid or liquid biological matrix. In addition, the technique is helpful in quantifying and optimizing the correct storage time of the pro-biotics, if they are entrapped in matrices such as alginate and follow their survival rate in simulated gastro-intestinal conditions. A second technique with great chances is the “biofilm electrostatic test” (BET). BET undoubtedly represents a fast, simple, and highly reproducible tool suitable for admitting the evaluation of the in vitro bacterial capacity in order to adhere through an electrostatic interaction with a pyro-electrified carrier after only 2 h of incubation. BET could represent the way for a quick and standardized evaluation of bacterial resistance among biofilm-producing microorganisms through a fast evaluation of the potential presence of the biofilm.
Collapse
|
9
|
Guo C, Jiang S, Song P, Wang T, Shao X, Zhang Z, Zheng G. Quantitative multi-height phase retrieval via a coded image sensor. BIOMEDICAL OPTICS EXPRESS 2021; 12:7173-7184. [PMID: 34858708 PMCID: PMC8606130 DOI: 10.1364/boe.443528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/01/2023]
Abstract
Multi-height phase retrieval introduces different object-to-detector distances for obtaining phase diversity measurements. In the acquisition process, the slow-varying phase information, however, cannot be converted to intensity variations for detection. Therefore, the low-frequency contents of the phase profile are lost during acquisition and cannot be properly restored via phase retrieval. Here, we demonstrate the use of a coded image sensor for addressing this challenge in multi-height phase retrieval. In our scheme, we add a coded layer on top of the image sensor for encoding the slow-varying complex wavefronts into intensity variations of the modulated patterns. Inspired by the concept of blind ptychography, we report a reconstruction scheme to jointly recover the complex object and the unknown coded layer using multi-height measurements. With both simulation and experimental results, we show that the recovered phase is quantitative and the slow-varying phase profiles can be properly restored using lensless multi-height measurements. We also show that the image quality using the coded sensor is better than that of a regular image sensor. For demonstrations, we validate the reported scheme with various biospecimens and compare the results to those of regular lensless multi-height phase retrieval. The use of a coded image sensor may enable true quantitative phase imaging for the lensless multi-height, multi-wavelength, and transport-of-intensity equation approaches.
Collapse
Affiliation(s)
- Chengfei Guo
- Xi'an Key Laboratory of Computational Imaging, Xidian University, Shaanxi 710071, China
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Shaowei Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Pengming Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Tianbo Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Xiaopeng Shao
- Xi'an Key Laboratory of Computational Imaging, Xidian University, Shaanxi 710071, China
| | - Zibang Zhang
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, China
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
10
|
Meteyer E, Foucart F, Pezerat C, Picart P. Modeling of speckle decorrelation in digital Fresnel holographic interferometry. OPTICS EXPRESS 2021; 29:36180-36200. [PMID: 34809036 DOI: 10.1364/oe.438346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
This paper presents analytical modeling of the speckle decorrelation noise in digital Fresnel holographic interferometry. The theoretical analysis is carried out by considering the complex coherence factor between two speckled images from two digitally reconstructed holograms at two different instants. The expression giving the modulus of the coherence factor is established and depends on the local surface deformation and parameters from the holographic setup. The analysis is supported by realistic simulations and experiments. Both simulations and experimental results exhibit a very good agreement with the theoretical prediction.
Collapse
|
11
|
Wang Z, Bianco V, Pirone D, Memmolo P, Villone MM, Maffettone PL, Ferraro P. Dehydration of plant cells shoves nuclei rotation allowing for 3D phase-contrast tomography. LIGHT, SCIENCE & APPLICATIONS 2021; 10:187. [PMID: 34526484 PMCID: PMC8443563 DOI: 10.1038/s41377-021-00626-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/15/2021] [Accepted: 08/27/2021] [Indexed: 05/07/2023]
Abstract
Single-cell phase-contrast tomography promises to become decisive for studying 3D intracellular structures in biology. It involves probing cells with light at wide angles, which unfortunately requires complex systems. Here we show an intriguing concept based on an inherent natural process for plants biology, i.e., dehydration, allowing us to easily obtain 3D-tomography of onion-epidermal cells' nuclei. In fact, the loss of water reduces the turgor pressure and we recognize it induces significant rotation of cells' nuclei. Thanks to the holographic focusing flexibility and an ad-hoc angles' tracking algorithm, we combine different phase-contrast views of the nuclei to retrieve their 3D refractive index distribution. Nucleolus identification capability and a strategy for measuring morphology, dry mass, biovolume, and refractive index statistics are reported and discussed. This new concept could revolutionize the investigation in plant biology by enabling dynamic 3D quantitative and label-free analysis at sub-nuclear level using a conventional holographic setup.
Collapse
Affiliation(s)
- Zhe Wang
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Vittorio Bianco
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università degli Studi di Napoli "Federico II", via Claudio 21, 80125, Napoli, Italy
| | - Pasquale Memmolo
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Massimiliano Maria Villone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pietro Ferraro
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| |
Collapse
|
12
|
Mojiri S, Isbaner S, Mühle S, Jang H, Bae AJ, Gregor I, Gholami A, Enderlein J. Rapid multi-plane phase-contrast microscopy reveals torsional dynamics in flagellar motion. BIOMEDICAL OPTICS EXPRESS 2021; 12:3169-3180. [PMID: 34221652 PMCID: PMC8221972 DOI: 10.1364/boe.419099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 05/23/2023]
Abstract
High speed volumetric optical microscopy is an important tool for observing rapid processes in living cells or for real-time tracking of sub-cellular components. However, the 3D imaging capability often comes at the price of a high technical complexity of the imaging system and/or the requirement of demanding image analysis. Here, we propose a combination of conventional phase-contrast imaging with a customized multi-plane beam-splitter for enabling simultaneous acquisition of images in eight different focal planes. Our method is technically straightforward and does not require complex post-processing image analysis. We apply our multi-plane phase-contrast microscope to the real-time observation of the fast motion of reactivated Chlamydomonas axonemes with sub-µm spatial and 4 ms temporal resolution. Our system allows us to observe not only bending but also the three-dimensional torsional dynamics of these micro-swimmers.
Collapse
Affiliation(s)
- Soheil Mojiri
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Sebastian Isbaner
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Steffen Mühle
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Hongje Jang
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Albert Johann Bae
- Max-Planck-Institute for
Dynamics and Self-Organization, 37077 Göttingen,
Germany
| | - Ingo Gregor
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Azam Gholami
- Max-Planck-Institute for
Dynamics and Self-Organization, 37077 Göttingen,
Germany
- Cluster of Excellence “Multiscale
Bioimaging: from Molecular Machines to Networks of Excitable
Cells” (MBExC),
Georg-August-University, 37077
Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| |
Collapse
|
13
|
Hansford DJ, Jin Y, Elston SJ, Morris SM. Enhancing laser speckle reduction by decreasing the pitch of a chiral nematic liquid crystal diffuser. Sci Rep 2021; 11:4818. [PMID: 33649413 PMCID: PMC7921095 DOI: 10.1038/s41598-021-83860-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/04/2021] [Indexed: 11/26/2022] Open
Abstract
The artefact known as speckle can plague numerous imaging applications where the narrow linewidth of laser light is required, which includes laser projection and medical imaging. Here, we report on the use of thin-film chiral nematic liquid crystal (LC) devices that can be used to mitigate the influence of speckle when subjected to an applied electric field. Results are presented which show that the speckle contrast (a quantitative measure of the presence of speckle) can be significantly reduced by decreasing the pitch of the chiral nematic LC from 2700 to 244 nm. Further reduction in the speckle contrast can be observed by operating the diffuser technology at a temperature close to the chiral nematic to isotropic transition. At such temperatures, we observe a simultaneous improvement in the transmission of light through the device and a decrease in the electric field amplitude required for the minimum speckle contrast value. We conclude by presenting a laser projected image of the 1951 USAF target with and without the LC device to demonstrate the visual improvement as a result of the speckle reduction.
Collapse
Affiliation(s)
- David J Hansford
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, UK
| | - Yihan Jin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, UK
| | - Steve J Elston
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, UK
| | - Stephen M Morris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, UK.
| |
Collapse
|
14
|
Lin W, Chen L, Cai W, Hu Y, Wen K. Speckle reduction in digital holography with low-dimensional reconstruction. APPLIED OPTICS 2021; 60:1470-1475. [PMID: 33690593 DOI: 10.1364/ao.414773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Speckle reduction is a crucial technique since the presence of speckle disturbs the quality of the reconstruction in digital holography. In this paper, we present an easy, fast, and efficient single-shot method to reduce speckle noise in digital holography. The method reconstructs subholograms from a single hologram. Then, sub-reconstruction images are randomly shuffled and divided into several groups and low-dimensional noise-reduced images can be achieved by averaging sub-reconstruction image groups by groups. Next, these low-dimensional noise-reduced images are combined to obtain a noise-reduced image. Finally, the noise-reduced image is processed by a mean filter to obtain a final image, which has substantially less speckle noise while preserving the dimensions of the original image. The experimental results demonstrate the effectiveness of the proposed method and indicate its potential in real-time digital holography.
Collapse
|
15
|
Stoykova E, Nazarova D, Nedelchev L, Blagoeva B, Berberova N, Hong K, Park J. Quantization of dynamic speckle patterns with spatially varying statistics. APPLIED OPTICS 2021; 60:A155-A165. [PMID: 33690365 DOI: 10.1364/ao.405991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/09/2020] [Indexed: 06/12/2023]
Abstract
Raw data compression is mandatory for monitoring of processes by dynamic speckle analysis when two-dimensional activity maps are built by pointwise statistical processing of correlated speckle patterns formed on the surface of diffusely reflecting objects under laser illumination. Coarse quantization of speckle patterns enables storage and transfer of a huge amount of images, but it may be inefficient at spatially varying speckle statistics, such as for patterns recorded at non-uniform illumination or reflectivity. We prove efficacy of coarse quantization of the raw speckle data with varying statistics for a normalized algorithm by simulation and a polymer drop drying experiment. Both uniform and non-uniform quantization are proposed for treating such data. Decreasing the bit depth from 8 to 3 is possible without worsening the quality of the activity map.
Collapse
|
16
|
Lin W, Chen L, Chen Y, Cai W, Hu Y, Wen K. Single-shot speckle reduction by elimination of redundant speckle patterns in digital holography. APPLIED OPTICS 2020; 59:5066-5072. [PMID: 32543505 DOI: 10.1364/ao.390500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Speckle reduction is a crucial technique, since the presence of speckle disturbs the quality of the reconstruction in digital holography. In this paper, we present a redundant speckle elimination method to suppress the speckle noise. For the same position in each of the reconstructed sub-images, we consider pixels with the same gray value as information with the same speckle distribution. Therefore, a speckle-suppressed gray value can be obtained by extracting pixels with different gray values and then averaging. Through theoretical analysis and experiments, we demonstrate that speckle contrast can be decreased significantly by using the proposed method. Moreover, we show that the despeckle strength of the proposed method highly depends on the number of binary masks. These results indicate the potential of the proposed method for various applications.
Collapse
|
17
|
Zhang H, Liu S, Cao L, Brady DJ. Noise suppression for ballistic-photons based on compressive in-line holographic imaging through an inhomogeneous medium. OPTICS EXPRESS 2020; 28:10337-10349. [PMID: 32225621 DOI: 10.1364/oe.385992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
Noise suppression is one of the most important tasks in imaging through inhomogeneous mediums. Here, we proposed a denoising approach based on compressive in-line holography for imaging through an inhomogeneous medium. A reference-beam-free system with a low-cost continuous-wave laser is presented. The suppression against the noise, which is brought by the scattering photons, is presented in simulations using the proposed algorithm. The noise immunity is demonstrated in lensless imaging behind a random phase mask with an optical depth of 1.42 by single exposure, as well as behind a ground glass with an optical depth of 6.38 by multiple exposures.
Collapse
|
18
|
Park S, Ahn JW, Jo Y, Kang HY, Kim HJ, Cheon Y, Kim JW, Park Y, Lee S, Park K. Label-Free Tomographic Imaging of Lipid Droplets in Foam Cells for Machine-Learning-Assisted Therapeutic Evaluation of Targeted Nanodrugs. ACS NANO 2020; 14:1856-1865. [PMID: 31909985 DOI: 10.1021/acsnano.9b07993] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Lipid droplet (LD) accumulation, a key feature of foam cells, constitutes an attractive target for therapeutic intervention in atherosclerosis. However, despite advances in cellular imaging techniques, current noninvasive and quantitative methods have limited application in living foam cells. Here, using optical diffraction tomography (ODT), we performed quantitative morphological and biophysical analysis of living foam cells in a label-free manner. We identified LDs in foam cells by verifying the specific refractive index using correlative imaging comprising ODT integrated with three-dimensional fluorescence imaging. Through time-lapse monitoring of three-dimensional dynamics of label-free living foam cells, we precisely and quantitatively evaluated the therapeutic effects of a nanodrug (mannose-polyethylene glycol-glycol chitosan-fluorescein isothiocyanate-lobeglitazone; MMR-Lobe) designed to affect the targeted delivery of lobeglitazone to foam cells based on high mannose receptor specificity. Furthermore, by exploiting machine-learning-based image analysis, we further demonstrated therapeutic evaluation at the single-cell level. These findings suggest that refractive index measurement is a promising tool to explore new drugs against LD-related metabolic diseases.
Collapse
Affiliation(s)
- Sangwoo Park
- Gwangju Center , Korea Basic Science Institute (KBSI) , Gwangju , 61186 , Korea
| | - Jae Won Ahn
- Department of Systems Biotechnology , Chung-Ang University , Anseong , Gyeonggi 17546 , Korea
| | - YoungJu Jo
- Department of Physics , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon , 34141 , Korea
- KAIST Institute for Health Science and Technology, KAIST , Daejeon , 34141 , Korea
| | - Ha-Young Kang
- Gwangju Center , Korea Basic Science Institute (KBSI) , Gwangju , 61186 , Korea
| | - Hyun Jung Kim
- Cardiovascular Center , Korea University Guro Hospital , Seoul , 08308 , Korea
| | - Yeongmi Cheon
- Gwangju Center , Korea Basic Science Institute (KBSI) , Gwangju , 61186 , Korea
| | - Jin Won Kim
- Cardiovascular Center , Korea University Guro Hospital , Seoul , 08308 , Korea
| | - YongKeun Park
- Department of Physics , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon , 34141 , Korea
- KAIST Institute for Health Science and Technology, KAIST , Daejeon , 34141 , Korea
- Tomocube Inc. , Daejeon , 34051 , Korea
| | - Seongsoo Lee
- Gwangju Center , Korea Basic Science Institute (KBSI) , Gwangju , 61186 , Korea
| | - Kyeongsoon Park
- Department of Systems Biotechnology , Chung-Ang University , Anseong , Gyeonggi 17546 , Korea
| |
Collapse
|
19
|
Yu C, Ji F, Xue J, Wang Y. Fringe Phase-Shifting Field Based Fuzzy Quotient Space-Oriented Partial Differential Equations Filtering Method for Gaussian Noise-Induced Phase Error. SENSORS 2019; 19:s19235202. [PMID: 31783649 PMCID: PMC6928610 DOI: 10.3390/s19235202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 11/07/2022]
Abstract
Traditional filtering methods only focused on improving the peak signal-to-noise ratio of the single fringe pattern, which ignore the filtering effect on phase extraction. Fringe phase-shifting field based fuzzy quotient space-oriented partial differential equations filtering method is proposed to reduce the phase error caused by Gaussian noise while filtering. First, the phase error distribution that is caused by Gaussian noise is analyzed. Furthermore, by introducing the fringe phase-shifting field and the theory of fuzzy quotient space, the modified filtering direction can be adaptively obtained, which transforms the traditional single image filtering into multi-image filtering. Finally, the improved fourth-order oriented partial differential equations with fidelity item filtering method is established. Experiments demonstrated that the proposed method achieves a higher signal-to-noise ratio and lower phase error caused by noise, while also retaining more edge details.
Collapse
Affiliation(s)
- Changzhi Yu
- Institute of Mechanical Manufacturing Technology, China Academy of Engineering Physics, Mianyang 621999, China;
| | - Fang Ji
- Institute of Mechanical Manufacturing Technology, China Academy of Engineering Physics, Mianyang 621999, China;
- Correspondence: (F.J.); (J.X.); Tel.: +86-0816-248-7676 (F.J.)
| | - Junpeng Xue
- School of Aeronautics and Astronautics, Sichuan University, Chengdu 610065, China
- Correspondence: (F.J.); (J.X.); Tel.: +86-0816-248-7676 (F.J.)
| | - Yajun Wang
- State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan 430079, China;
| |
Collapse
|
20
|
Picart P, Montresor S. Contrast transfer function of de-noising algorithms. OPTICS EXPRESS 2019; 27:23336-23356. [PMID: 31510613 DOI: 10.1364/oe.27.023336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
This paper presents a comprehensive study on the contrast transfer function of de-noising algorithms. In order to cover a broad variety of methods, 45 de-noising algorithms are chosen considering their recognized efficiency in the different application domains of image processing. Advanced methods are targeted: wavelet transform-based algorithms with Daubechies, symlets, curvelets, contourlets, patch-based methods such as BM3D, NL-means algorithms and deep learning approaches; in addition, classical spatial filtering methods are considered, such as Wiener, median, Gauss filtering, and adaptive filtering approaches such as anisotropic diffusion and synthetic aperture radar filtering. The contrast transfer function is provided for each algorithm. Ranking of the set of de-noising algorithms is established according to proposed metrics. The paper provides practical methodology and novel results dedicated to the evaluation of the contrast transfer function of de-noising approaches from literature.
Collapse
|