Classification of cell morphology with quantitative phase microscopy and machine learning.

We describe and compare two machine learning approaches for cell classification based on label-free quantitative phase imaging with transport of intensity equation methods. In one approach, we design a multilevel integrated machine learning classifier including various individual models such as artificial neural network, extreme learning machine and generalized logistic regression. In another approach, we apply a pretrained convolutional neural network using transfer learning for the classification. As a validation, we show the performances of both approaches on classification between macrophages cultured in normal gravity and microgravity with quantitative phase imaging. The multilevel integrated classifier achieves average accuracy 93.1%, which is comparable to the average accuracy 93.5% obtained by convolutional neural network. The presented quantitative phase imaging system with two classification approaches could be helpful to biomedical scientists for easy and accurate cell analysis.

[1]  Jianlin Zhao,et al.  Quantitative phase microscopy for cellular dynamics based on transport of intensity equation. , 2018, Optics express.

[2]  Jianlin Zhao,et al.  Quantitative investigation on morphology and intracellular transport dynamics of migrating cells. , 2019, Applied optics.

[3]  Can Fahrettin Koyuncu,et al.  Smart Markers for Watershed-Based Cell Segmentation , 2012, PloS one.

[4]  YongKeun Park,et al.  Measuring cell surface area and deformability of individual human red blood cells over blood storage using quantitative phase imaging , 2016, Scientific Reports.

[5]  Baoli Yao,et al.  DMD-based LED-illumination Super-resolution and optical sectioning microscopy , 2013, Scientific Reports.

[6]  Pinhas Girshovitz,et al.  Generalized cell morphological parameters based on interferometric phase microscopy and their application to cell life cycle characterization , 2012, Biomedical optics express.

[7]  Jiawei Wu,et al.  Two-dimensional clinorotation influences cellular morphology, cytoskeleton and secretion of MLO-Y4 osteocyte-like cells , 2011, Biologia.

[8]  A. Asundi,et al.  Noninterferometric single-shot quantitative phase microscopy. , 2013, Optics letters.

[9]  Peng Shang,et al.  Digital holographic microscopy long-term and real-time monitoring of cell division and changes under simulated zero gravity. , 2012, Optics express.

[10]  Xiaobo Tian,et al.  Multi-wavelength quantitative polarization and phase microscope. , 2019, Biomedical optics express.

[11]  Balpreet Singh Ahluwalia,et al.  Partially spatially coherent digital holographic microscopy and machine learning for quantitative analysis of human spermatozoa under oxidative stress condition , 2019, Scientific Reports.

[12]  Sandeep Rathor,et al.  Acoustic domain classification and recognition through ensemble based multilevel classification , 2019, J. Ambient Intell. Humaniz. Comput..

[13]  A. E. Vasdekis,et al.  Robust microbial cell segmentation by optical‐phase thresholding with minimal processing requirements , 2017, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[14]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[15]  Jonghee Yoon,et al.  Holographic deep learning for rapid optical screening of anthrax spores , 2017, Science Advances.

[16]  A. Asundi,et al.  Boundary-artifact-free phase retrieval with the transport of intensity equation: fast solution with use of discrete cosine transform. , 2014, Optics express.

[17]  Euan A. Ashley,et al.  Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments , 2016, PLoS Comput. Biol..

[18]  Tomi Pitkäaho,et al.  Focus prediction in digital holographic microscopy using deep convolutional neural networks. , 2019, Applied optics.

[19]  Radim Chmelik,et al.  Automated classification of cell morphology by coherence-controlled holographic microscopy. , 2017, Journal of biomedical optics.

[20]  Alamelu Sundaresan,et al.  The impact of microgravity on bone in humans. , 2016, Bone.

[21]  Jianlin Zhao,et al.  Quantitative and Dynamic Phase Imaging of Biological Cells by the Use of the Digital Holographic Microscopy Based on a Beam Displacer Unit , 2018, IEEE Photonics Journal.

[22]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[23]  Pramod Kumar Srivastava,et al.  Reagent-Free and Rapid Assessment of T Cell Activation State Using Diffraction Phase Microscopy and Deep Learning. , 2019, Analytical chemistry.

[24]  Ata Mahjoubfar,et al.  Deep Learning in Label-free Cell Classification , 2016, Scientific Reports.

[25]  M. Teague Deterministic phase retrieval: a Green’s function solution , 1983 .

[26]  Oliver Ullrich,et al.  Real-Time Video-Microscopy of Migrating Immune Cells in Altered Gravity During Parabolic Flights , 2010 .

[27]  Jianlin Zhao,et al.  Dual-wavelength common-path digital holographic microscopy for quantitative phase imaging of biological cells , 2017 .

[28]  Min Xu,et al.  Lung cancer diagnosis with quantitative DIC microscopy and a deep convolutional neural network. , 2019, Biomedical optics express.

[29]  Ciyuan Qiu,et al.  Automated Wavelength Alignment in a 4 × 4 Silicon Thermo-Optic Switch Based on Dual-Ring Resonators , 2018, IEEE Photonics Journal.

[30]  Dalip Singh Mehta,et al.  Development of full-field optical spatial coherence tomography system for automated identification of malaria using the multilevel ensemble classifier. , 2018, Journal of biophotonics.

[31]  A. Asundi,et al.  High-resolution transport-of-intensity quantitative phase microscopy with annular illumination , 2017, Scientific Reports.

[32]  T. Gureyev,et al.  Phase retrieval using radiation and matter-wave fields: Validity of Teague's method for solution of the transport-of-intensity equation , 2011 .

[33]  Christian Depeursinge,et al.  Quantitative phase imaging in biomedicine , 2018, Nature Photonics.

[34]  T N Belyaeva,et al.  In vitro monitoring of photoinduced necrosis in HeLa cells using digital holographic microscopy and machine learning. , 2020, Journal of the Optical Society of America. A, Optics, image science, and vision.

[35]  Bahram Javidi,et al.  Automated segmentation of multiple red blood cells with digital holographic microscopy , 2013, Journal of biomedical optics.

[36]  Jochen Guck,et al.  Bacterial infection of macrophages induces decrease in refractive index , 2013, Journal of biophotonics.

[37]  Yibo Zhang,et al.  PhaseStain: the digital staining of label-free quantitative phase microscopy images using deep learning , 2018, Light: Science & Applications.

[38]  Thomas Schneider,et al.  Fourier-based solving approach for the transport-of-intensity equation with reduced restrictions. , 2018, Optics express.

[39]  George Nehmetallah,et al.  Quantitative assessment of cancer cell morphology and motility using telecentric digital holographic microscopy and machine learning , 2018, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[40]  Cheng Lei,et al.  Label-free detection of cellular drug responses by high-throughput bright-field imaging and machine learning , 2017, Scientific Reports.

[41]  Mona Mihailescu,et al.  Changes in optical properties of electroporated cells as revealed by digital holographic microscopy. , 2017, Biomedical optics express.

[42]  J. Petruccelli,et al.  Source diversity for transport of intensity phase imaging. , 2017, Optics express.

[43]  F. Zernike How I discovered phase contrast. , 1955, Science.

[44]  Hyun-seok Min,et al.  Quantitative Phase Imaging and Artificial Intelligence: A Review , 2018, IEEE Journal of Selected Topics in Quantum Electronics.

[45]  Kavita Dubey,et al.  Automated assessment of breast cancer margin in optical coherence tomography images via pretrained convolutional neural network , 2018, Journal of biophotonics.

[46]  Nicolas Pavillon,et al.  Noninvasive detection of macrophage activation with single-cell resolution through machine learning , 2018, Proceedings of the National Academy of Sciences.

[47]  Wen Xiao,et al.  Quantitative observations on cytoskeleton changes of osteocytes at different cell parts using digital holographic microscopy. , 2018, Biomedical optics express.