Tomographic diffractive microscopy: Towards high-resolution 3-D real-time data acquisition, image reconstruction and display of unlabeled samples

Bailleul, Jonathan; Simon, Bertrand; Debailleul, Matthieu; Foucault, Ludovic; Verrier, Nicolas; Haeberlé, Olivier

doi:10.1016/j.optcom.2017.11.008

Cited by 20 publications

(11 citation statements)

References 80 publications

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“…Advantages of such techniques include the capability of virtual instead of physical sectioning and the possibility of quantitative 3D analysis in the original geometry. It is also possible to do 3D imaging of unlabeled samples making use of intrinsic contrast present in the sample [1,2]. One such contrast is the refractive index (RI) variation in the sample, which is often feature specific and provides information about the global structure in the sample (in contrast to molecular specific techniques).…”

Section: Introductionmentioning

confidence: 99%

Large-scale high-sensitivity optical diffraction tomography of zebrafish

Rooij¹,

Kalkman²

2019

Biomed. Opt. Express

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In this work we demonstrate large-scale high-sensitivity optical diffraction tomography (ODT) of zebrafish. We make this possible by three improvements. First, we obtain a large field of view while still maintaining a high resolution by using a high magnification over numerical aperture ratio digital holography setup. With the inclusion of phase shifting we operate close to the optimum magnification over numerical aperture ratio. Second, we decrease the noise in the reconstructed images by implementing off-axis sample placement and numerical focus tracking in combination with the acquisition of a large number of projections. Although both techniques lead to an increase in sensitivity independently, we show that combining them is necessary in order to make optimal use of the potential gain offered by each respective method and obtain a refractive index (RI) sensitivity of 8 • 10 −5. Third, we optimize the optical clearing procedure to prevent scattering and refraction to occur. We demonstrate our technique by imaging a zebrafish larva over 13 mm 3 field of view with 4 micrometer resolution. Finally, we demonstrate a clinical application of our technique by imaging an entire adult cryoinjured zebrafish heart.

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Section: Introductionmentioning

confidence: 99%

Large-scale high-sensitivity optical diffraction tomography of zebrafish

Rooij¹,

Kalkman²

2019

Biomed. Opt. Express

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“…Also, its computational nature limits final 3-D image delivery rate. But high-speed acquisitions are possible [26], and modern GPUs also allow for high-speed reconstructions [27], the present bottleneck being the data transfer rate between camera and computer. Several groups are also active in developing simplified, lowcost approaches [28] [29], and TDM in reflection mode, not developed in this summary, also present advantages compared to standard optical microscopy, even with simple image reconstruction approaches [30].…”

Section: Discussionmentioning

confidence: 99%

Tomographic diffractive microscopy: principles and applications

Haeberlé

2018

Unconventional Optical Imaging

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Tomographic Diffractive Microscopy (TDM) is an advanced digital imaging technique, extending the concept of Digital Holographic Microscopy (DHM), which provides quantitative information about the index of refraction distribution within the observed sample, by recording of multiple holograms under varying conditions of illumination, then applying numerical inversion procedures to reconstruct a 3-D image of the specimen under consideration. After a short recall of DHM applications and limitations, various implementations of TDM are described, highlighting their respective advantages and. drawbacks. To conclude, some perspectives and challenges for this imaging modality are presented.

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“…non-smooth part H (26) where the smooth part G correponds to the data-fidelity term J fid in Eq. (24) and the non-smooth part H is the indicator function ι O in Eq.…”

Section: The Alternating Projections Point Of Viewmentioning

confidence: 99%

“…(27) and Eq. (26). We illustrate the convergence of the RI method with several optimization strategies: FISTA, ISTA, and VMLMB [64,65], a quasi-Newton gradient Variable Metric method with Limited Memory requirements and possibly Bound constraints enforcement on the unknowns.…”

Section: Reconstruction Parametersmentioning

confidence: 99%

“…Any appropriate optical model can then be used to describe how an incident illumination wave gets diffracted by the sample and propagates to the sensor: diffraction by a plane (Rayleigh-Sommerfeld, Fresnel approximation, angular spectrum) [20], diffraction by a volume (Born approximation, Rytov approximation) [21], diffraction by a sphere (Mie scattering) [22], free-space propagation. Multiple holograms can be recorded to improve information diversity by including lateral or axial shifts of the sensor [16,23], multiple illumination wavelengths [24], or multiple illumination angles [25,26]. When a suitable model of the observations has been defined, a "reconstruction" (or "estimation") method can be selected.…”

Section: Introductionmentioning

confidence: 99%

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From Fienup’s phase retrieval techniques to regularized inversion for in-line holography: tutorial

Momey¹,

Denis²,

Thomas³

et al. 2019

J. Opt. Soc. Am. A

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This paper includes a tutorial on how to reconstruct in-line holograms using an inverse problems approach, starting with modeling the observations, selecting regularizations and constraints, and ending with the design of a reconstruction algorithm. A special focus is made on the connections between the numerous alternating projection strategies derived from Fienup's phase retrieval technique and the inverse problems framework. In particular, an interpretation of Fienup's algorithm as iterates of a proximal gradient descent for a particular cost function is given. Reconstructions from simulated and experimental holograms of micrometric beads illustrate the theoretical developments. The results show that the transition from alternating projection techniques to the inverse problems formulation is straightforward and advantageous.

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Tomographic diffractive microscopy: Towards high-resolution 3-D real-time data acquisition, image reconstruction and display of unlabeled samples

Cited by 20 publications

References 80 publications

Large-scale high-sensitivity optical diffraction tomography of zebrafish

Large-scale high-sensitivity optical diffraction tomography of zebrafish

Tomographic diffractive microscopy: principles and applications

From Fienup’s phase retrieval techniques to regularized inversion for in-line holography: tutorial

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