Prof. Natan T. Shaked has received the

Chair (Cathedra) of Advanced Biomedical Optical Microscopy

in Tel Aviv University

Lecture title:
Deep2Deep: AI and deep learning for label-free 3D cell classification

https://spie.org/photonics-west/event/biophotonics-focus-ai-ml-dl-plenary/2656964

Prof. Shaked has been appointed as the Chair of the Department of Biomedical Engineering in Tel Aviv University (containing 15 research groups and ~500 undergraduate & graduate students).

[Link]

Gili Dardikman-Yoffe, Simcha K. Mirsky, Itay Barnea, and Natan T. Shaked

Abstract: We present a new acquisition method that enables high-resolution, fine-detail full reconstruction of the three-dimensional movement and structure of individual human sperm cells swimming freely. We achieve both retrieval of the three-dimensional refractive-index profile of the sperm head, revealing its fine internal organelles and time-varying orientation, and the detailed four-dimensional localization of the thin, highly-dynamic flagellum of the sperm cell. Live human sperm cells were acquired during free swim using a high-speed off-axis holographic system that does not require any moving elements or cell staining. The reconstruction is based solely on the natural movement of the sperm cell and a novel set of algorithms, enabling the detailed four-dimensional recovery. Using this refractive-index imaging approach, we believe we have detected an area in the cell that is attributed to the centriole. This method has great potential for both biological assays and clinical use of intact sperm cells.

Science Advances, Vol. 6, No. 15, eaay7619, 2020 [Link]

Download: [PDF, Supp Mat, Video 1, Video 2, Video 3, Video 4, Video 5]

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Rapid label-free refractive-index tomography of a sperm cell during free swim.

Prof. Shaked has been promoted to a Full Professor Rank.

Rapid three-dimensional refractive-index imaging of live cells in suspension without labeling using dielectrophoretic cell rotation

Mor Habaza, Michael Kirschbaum, Christian Guernth-Marschner, Gili Dardikman, Itay Barnea, Rafi Korenstein, Claus Duschl, and Natan T. Shaked

Abstract:

A major challenge in the field of optical imaging of live cells is achieving rapid, three-dimensional (3-D) and noninvasive imaging of isolated cells without labeling. If successful, many clinical procedures involving analysis and sorting of cells drawn from body fluids, including blood, can be significantly improved.  We present a new label-free tomographic interferometry approach that provides rapid capturing of the 3-D refractive index distribution of single cells in suspension. The cells flow in a microfluidic channel, are trapped and rapidly rotated by dielectrophoretic forces in a noninvasive and precise manner. Interferometric projections of the rotated cell are acquired and processed into the cellular 3-D refractive index map.  Uniquely, this approach provides full (360^o) coverage of the rotation angular range on any axis, and knowledge on the viewing angle. Our experimental demonstrations include 3-D, label-free imaging of both large cancer cells and three-types of white blood cells. This approach is expected to be useful for label-free cell sorting, as well as for detection and monitoring of pathological conditions resulting in cellular morphology changes or occurrence of contain cellular types in blood or other body fluids.

(a,b) Refractive-index maps of an MCF-7 cell at the mid-sagittal slice for using a full cell rotation on a single axis (a) and on two axes (b). The arrow indicate details that are clearer when rotating the cell on two axes.  (c,d) 3-D renderings (c) and rendered iso-surface plot (d) of the refractive-index map of the reconstructed refractive index map of an MCF-7 cancer cell. (e-j) Refractive index maps of three types of white blood cells at the mid-axial positions (e-g), and the coinciding rendered iso-surface plots of the refractive-index maps (h-j); (e,h) T cell, see also Supplementary Video 4; (f,i) Monocyte, see also Supplementary Video 5; (g,j) Neutrophil, see also Supplementary Video 6.

New paper accepted to Optics Express

New paper in Optics Express, 2016:

Video-rate processing in tomographic phase microscopy of biological cells using CUDA

Gili Dardikman, Mor Habaza, Laura Waller, and Natan T. Shaked

Abstract:

We suggest a new implementation for rapid reconstruction of three-dimensional (3-D) refractive index (RI) maps of biological cells acquired by tomographic phase microscopy (TPM). The TPM computational reconstruction process is extremely time consuming, making the analysis of large data sets unreasonably slow and the real-time 3-D visualization of the results impossible. Our implementation uses new phase extraction, phase unwrapping and Fourier slice algorithms, suitable for efficient CPU or GPU implementations. The experimental setup includes an external off-axis interferometric module connected to an inverted microscope illuminated coherently. We used single cell rotation by micro-manipulation to obtain interferometric projections from 73 viewing angles over a 180° angular range. Our parallel algorithms were implemented using Nvidia’s CUDA C platform, running on Nvidia’s Tesla K20c GPU. This implementation yields, for the first time to our knowledge, a 3-D reconstruction rate higher than video rate of 25 frames per second for 256 × 256-pixel interferograms with 73 different projection angles (64 × 64 × 64 output). This allows us to calculate additional cellular parameters, while still processing faster than video rate. This technique is expected to find uses for real-time 3-D cell visualization and processing, while yielding fast feedback for medical diagnosis and cell sorting.

[Link] [PDF]

Average reconstruction rates (fps) and speedups when comparing the CPU and GPU efficient implementations, for various input hologram sizes (a) Rates including reading and writing to/from the CPU and memory transfers to/from the GPU when relevant; (b) Rates not including reading and writing to/from the CPU. © 2016 OSA