Jin Chen

Research in Optical Imaging

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Peer-Reviewed Journal Articles

Jin Chen Qianqian Fang and Xavier Intes
Widefield Mesh-based Monte Carlo Method in time-domain Fluorescence Molecular Tomography
Journal of Biomedical Optics, under review.
Preprint Abstract
Abstract :
Vivek Venugopal, Jin Chen, M Barroso and Xavier Intes
NIR FRET Optical Tomography
Proceedings of the National Academy of Sciences, in preparation.
Preprint Abstract
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Jin Chen and Xavier Intes
Comparison of Monte Carlo methods for fluorescence molecular tomography - computational efficiecny
Medical Physics, Vol 38, Issue 10, pp. 5788-5798 (2011). (Selected for publication in the Virtual Journal for Biomedical Optics (VJBO))
Preprint Abstract
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Jin Chen, Vivek Venugopal and Xavier Intes
A Monte Carlo based method for fluorescence tomographic imaging with lifetime multiplexing using time gates
Biomedical Optics Express, Vol 2, Issue 4, pp. 871-886 (2011).
Preprint Abstract
Abstract : Time-resolved fluorescence optical tomography allows 3-dimensional localization of multiple fluorophores based on lifetime contrast while providing a unique data set for improved resolution. However, to employ the full fluorescence time measurements, a light propagation model that accurately simulates weakly diffused and multiple scattered photons is required. In this article, we derive a computationally efficient Monte Carlo based method to compute time-gated fluorescence Jacobians for the simultaneous imaging of two fluorophores with lifetime contrast. The Monte Carlo based formulation is validated on a synthetic murine model simulating the uptake in the kidneys of two distinct fluorophores with lifetime contrast. Experimentally, the method is validated using capillaries filled with 2.5nmol of ICG and IRDye™800CW respectively embedded in a diffuse media mimicking the average optical properties of mice. Combining multiple time gates in one inverse problem allows the simultaneous reconstruction of multiple fluorophores with increased resolution and minimal crosstalk using the proposed formulation.
Vivek Venugopal, Jin Chen and Xavier Intes
Development of an optical imaging platform for functional imaging of small animals using wide-field excitation
Biomedical Optics Express, Vol 1, Issue 1, pp. 143 (2010).
Preprint Abstract
Abstract : The design and characterization of a time-resolved functional imager using a wide-field excitation scheme for small animal imaging is described. The optimal operation parameters are established based on phantom studies. The performance of the platform for functional imaging and the simultaneous 3D reconstruction of absorption and scattering coefficients is investigated in vitro.
Vivek Venugopal, Jin Chen, Frederic Lesage and Xavier Intes
Full-field time-resolved fluorescence tomography of small animals
Optics Letters, Vol 35, Issue 19, pp. 3189-3191 (2010).
Preprint Abstract
Abstract :In this experimental investigation, we explore the feasibility of using wide-field illumination for time-resolved fluorescence molecular tomography. The performance of wide-field patterns with a time-resolved imaging platform is investigated in vitro and in a small animal model. A Monte Carlo-based forward model is employed to reconstruct fluorescence yield based on time-gated datasets. An improvement in resolution and quantification when using the time-gate data type compared to the commonly used cw data type is demonstrated in vitro. Furthermore, the feasibility of wide-field strategies for fluorescence preclinical applications is established by an accurate localization of a fluorescent inclusion implanted in the chest cavity of a murine model.
Jin Chen, Vivek Venugopal, Frederic Lesage and Xavier Intes
Time-resolved diffuse optical tomography with patterned-light illumination and detection
Optics Letters, Vol. 35, Issue 13, pp. 2121-2123 (2010). (Selected for publication in the Virtual Journal for Biomedical Optics (VJBO))
Preprint Abstract
Abstract : This investigation explores the feasibility of performing diffuse optical tomography based on time-domain wide-field illumination and detection strategies. Wide-field patterned excitation and detection schemes are investigated in transmittance geometry with time-gated detection channels. A Monte Carlo forward model is employed to compute the time-resolved Jacobians for rigorous light propagation modeling. We demonstrate both in silico and experimentally that reconstructions of absorption structures based on wide-field patterned-light strategies are feasible and outperform classical point excitation schemes for similar data set sizes. Moreover, we demonstrate that time-domain information is retained even though large spatial areas are illuminated. The enhanced time-domain data set allows for quantitative three-dimensional imaging in thick tissue based on relatively small data sets associated with much shorter acquisition times.
Jin Chen and Xavier Intes
Time-gated perturbation Monte Carlo for whole body functional imaging in small animals
Optics Express, Vol 17, Issue 22, pp. 19566-19579 (2009).
Preprint Abstract
Abstract : This paper explores a time-resolved functional imaging method based on Monte Carlo model for whole-body functional imaging of small animals. To improve the spatial resolution and quantitative accuracy of the functional map, a Bayesian hierarchical method with a high resolution spatial prior is applied to guide the optical reconstructions. Simulated data using the proposed approach are employed on an anatomically accurate mouse model where the optical properties range and volume limitations of the diffusion equation model exist. We investigate the performances of using time-gated data type and spatial priors to quantitatively image the functional parameters of multiple organs. Accurate reconstructions of the two main functional parameters of the blood volume and the relative oxygenation are demonstrated by using our method. Moreover, nonlinear optode settings guided by anatomical prior is proved to be critical to imaging small organs such as the heart.
Yun Jing, Jin Chen, Xiao Chen and Xun Gong
Frequency shift of thickness-shear vibrations of AT-cut quartz resonators due to a liquid layer with the electrode stiffness considered
IEEE transactions on ultrasonics, ferroelectrics, and frequency control, Vol 54, Issue 7, pp. 1290-1292 (2007).
Preprint Abstract
Abstract : Thickness-shear vibrations of an AT-cut quartz resonator due to a liquid layer are studied. Closed form solutions are obtained with electrodes considered. Effect of the shear stiffness of electrodes on frequency shifts is presented.
Yun Jing, Jin Chen, Xun Gong and Jie Duan
Stress-induced frequency shifts in rotated Y-cut langasite resonators with electrodes considered
IEEE transactions on ultrasonics, ferroelectrics, and frequency control, Vol 54, Issue 5, pp. 906-909 (2007).
Preprint Abstract
Abstract : Stress-induced frequency shifts of the thickness-shear vibration of rotated Y-cut langasite resonators are studied with the electrode considered. The relationship between mass loading and force-frequency coefficients is explored for several kinds of electrode materials. Comparisons between Y-cut langasite and AT-cut quartz resonators are also presented.

Journal Articles in Preparation

Jin Chen and Xavier Intes
Mesh-model and datatype optimization in diffuse optics tomography
in preparation.
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Book Chapter

Xavier Intes, Vivek Venugopal, Jin Chen and Fred Azar
Multimodal diffuse imaging system
Biomedical Optical Imaging Techniques: Design and Applications, Springer, in press, Spring 2012.
Preprint Abstract
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Conference Proceedings Papers

Jin Chen and Xavier Intes
Wide-field Mesh-based Monte Carlo method in time-domain Fluorescence Molecular Tomography
In Biomedical Optics, OSA Techinical Digest (CD) (Optical Society of America, 2012).
Preprint Abstract
Abstract :
Jin Chen and Xavier Intes
Mesh-based Monte Carlo method for time-gated optical tomography
Proceedings of the IEEE 37th Annual Northeast Bioengineering Conference, Rensselaer Polytechinic Institute, Troy, USA, April 2011.
Preprint Abstract
Abstract : We describe a novel mesh-based Monte Carlo optical reconstruction algorithm for time-gated 3D optical tomography in small animals. Compared with previous works using voxel-based media discretization, a mesh-based approach is more accurate in modeling targets with curved boundaries or locally refined structures. Using an efficient ray-tracing technique, the mesh-based Monte Carlo method enables us to model both media properties and fluence distribution. Excellent agreement is found when comparing mesh-based MC with 3D voxel-based MC code in a synthetic mouse model.
Vivek Venogupal, Jin Chen and Xavier Intes
Adaptive correction of dynamic range in small animal wide-field fluorescence tomography
Proceedings of the IEEE 37th Annual Northeast Bioengineering Conference, Rensselaer Polytechinic Institute, Troy, USA, April 2011.
Preprint Abstract
Abstract : In this work, we present a measurement-guided pattern optimization scheme directed towards maximizing signal-noise-ratio in tomographic measurements by reducing the dynamic range in transmitted signal intensity in small animal models.
Vivek Venogupal, Jin Chen, M Barroso and Xavier Intes
In vivo reconstruction of NIR FRET using full-field time resolved optical tomography
Proceedings of the IEEE 37th Annual Northeast Bioengineering Conference, Rensselaer Polytechinic Institute, Troy, USA, April 2011.
Preprint Abstract
Abstract : We investigate the feasibility of 3-D localization of Foerster resonance energy transfer (FRET) between two NIR fluorophores (Alexa Fluor 700 and Alexa Fluor 750) in small animal models. Specifically, the decrease in donor lifetime upon FRET is used as the contrast mechanism to isolate donor-acceptor pairs undergoing FRET. The optical tomography system uses a femtosecond tunable laser coupled with a micro-mirror device based digital light processor as the source to generate wide-field patterns. The time-resolved detection is achieved using a gated intensified CCD camera. The wide-field excitation scheme described herein provides an experimental advantage by reducing the time of acquisition of temporally dense datasets. In this study, anatomical information obtained using MR imaging is used in the computation of the Monte Carlo (MC) based forward model. The MC model reconstructs the 3D distribution of the quantum yield of the donor fluorophore and the FRET complex using the time-gate data type allowing the estimation of fractional distribution (ıD) of donor molecules undergoing FRET and unquenched donor molecules. The performance of this approach in the estimation of ıD using the position of fluorophores obtained using the MRI is investigated.
M Pimpalkhare, Vivek Venugopal, Jin Chen and Xavier Intes
Anatomical segmentation for guided Flurenscence Molecular Tomography in small animals
Proceedings of the IEEE 37th Annual Northeast Bioengineering Conference, Rensselaer Polytechinic Institute, Troy, USA, April 2011.
Preprint Abstract
Abstract : In this work, we investigate the performances of segmentation algorithms applied to micro-CT images of small animal to derive anatomical templates for guided Fluorescence Molecular Tomography. We report on the performances of Active Contours methods to retrieve the boundary surface of the specimen and the internal distribution of a fluorescent probe. The spatial information gained from this segmentation procedure is used to cast an accurate light propagation forward model and used as spatial prior to constrain the optical inverse problem.
Jin Chen, Vivek Venugopal and Xavier Intes
Tomography in time-domain: Monte Carlo approaches and efficiency comparison
SPIE BIOS, Multimodal Biomedical Imaging, San Francisco, USA, January 2011.
Preprint Abstract
Abstract :
Vivek Venugopal, Jin Chen, M Barroso and Xavier Intes
In vivo reconstruction of NIR FRET using full-field time resolved optical tomography
In Proceedings of SPIE (2011), pp. 78920I-78920I-8.
Preprint Abstract
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Vivek Venugopal, Jin Chen, Frederic Lesage and Xavier Intes
Time Resolved Diffuse Optical Tomography using a Digital Light Processor
In Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2012), paper BSuD52.
Preprint Abstract
Abstract : We experimentally demonstrate that time-resolved measurements of broad spatial patterns transmitted through an optically heterogeneous medium retain their temporal characteristics providing robust signals for efficient decoupling of optical properties and allowing fast quantitative high-resolution reconstruction.
Jin Chen and Xavier Intes
Monte Carlo method for time-gated fluorescence tomography in small animals
In Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2012), paper BSuD95.
Preprint Abstract
Abstract : We investigated the performance of the time-gated Diffuse Optical Tomography based on Monte Carlo model with patterned wide-field illumination on a mouse model. The reconstructions outperform classical punctual excitation schemes for similar data sizes.
Jin Chen and Xavier Intes
Time gated optical imaging for functional and structural imaging
36th Annual Northeast Bioengineering Conference, Columbia University, New York, NY, USA, April 2010.
Preprint Abstract
Abstract : We investigated the performances of time-gated dataset to perform functional DOT in a synthetic murine model. The light propagation model used was based on the Monte Carlo method for accuracy. It is found that time-gates provide superior performances compared to classical approaches. Especially, time gates allow for efficient separation between absorption and scattering heterogeneities with minimal cross-talk.
Jin Chen, Vivek Venugopal and Xavier Intes
Towards time-resolved whole body optical imaging in small animals based on Monte Carlo method
Proceedings of the IEEE 36th Annual Northeast Bioengineering Conference, Columbia University, New York, USA, April 2010.
Preprint Abstract
Abstract :
Vivek Venugopal, Jin Chen and Xavier Intes
On the use of wide-field light patterns for small animal optical molecular imaging
Proceedings of the IEEE 36th Annual Northeast Bioengineering Conference, Columbia University, New York, USA, April 2010.
Preprint Abstract
Abstract :
Jin Chen, Vivek Venugopal and Xavier Intes
MRI Guided Preclinical Molecular Imaging in Time-domain: Perturbation Monte Carlo Approach
SPIE BIOS, Multimodal Biomedical Imaging, San Francisco, USA, January 2010.
Preprint Abstract
Abstract :
Vivek Venugopal, Jin Chen and Xavier Intes
A quantitative time domain functional imager for small animal studies
SPIE BIOS, Multimodal Biomedical Imaging, San Francisco, USA, January 2010.
Preprint Abstract
Abstract :
Jin Chen, Vivek Venugopal, and Xavier Intes
Diffuse optical tomography with time-gated perturbation Monte Carlo method
In Proceedings of SPIE, Vol.7171, 717113, San Jose, USA, January 2009.
Preprint Abstract
Abstract : Diffuse optical tomography using perturbation Monte Carlo method can overcome the drawback inherent to the classical model based on the diffusion equation for pre-clinical applications. The combined use of information from different time gates enables image reconstruction with accurate quantification and reducing the crosstalk between the absorption and the scattering coefficients. In this work, we apply this approach to solve an inverse problem of a 3D mouse model, and investigate the benefit to incorporate the time-resolved data into the optical reconstruction for quantitative functional imaging.
Vivek Venugopal, Jin Chen and Xavier Intes
Quantifying optical properties in small animals using MR-guided multispectral time-resolved imaging
In Proceedings of SPIE, Vol.7171, 717114, San Jose, USA, January 2009.
Preprint Abstract
Abstract : We propose the use of Time-Resolved Diffuse Optical Tomography in a multispectral scheme with anatomical constraints supplied by MR imaging to reconstruct functional parameters of the animal model with greater accuracy and resolution. The tomographic imaging system described is capable of acquiring temporal measurements in multiple-views using a gated ICCD camera. A tunable Ti-Sapphire pulsed laser at wavelengths between 700nm - 1000nm is used as the source. Anatomical distribution is determined using MRI in a non-concurrent setting. Time-resolved measurements at multiple wavelengths in the NIR window combined with the anatomical constraints is used to determine a 3D distribution of the functional parameters in vivo. Multispectral spectroscopy measurements on homogenous tissue simulating phantoms are used to demonstrate the accuracy of the system in determining optical parameters in thin tissues. We show that temporal measurements combined with MRI data can be used to accurately quantify optical properties in heterogeneous tissues.
Jin Chen and Xavier Intes
Time-gated perturbation Monte Carlo method for functional imaging of cancer
Conference on cancer genomics, Rensselaer, NY, USA, November 2008.
Preprint Abstract
Abstract : We developed a new optical time-gated forward model based on a perturbation Monte Carlo technique to perform 3D optical imaging in small animals. This new forward model overcomes many limitations encountered with the classical forward model based on the diffusion equation.
Jin Chen and Xavier Intes
Time-resolved perturbation Monte Carlo for 3D optical imaging in small animals
Proceedings of the IEEE 34th Annual Northeast Bioengineering Conference, Brown University, Providence, USA, April 2008.
Preprint Abstract
Abstract : We developed a new optical time-gated forward model based on a perturbation Monte Carlo technique to perform 3D optical imaging in small animals. This new forward model overcomes many limitations encountered with the classical forward model based on the diffusion equation.

Conference Abstracts

Vivek Venugopal, Jin Chen and Xavier Intes
A quantitative time domain functional imager for small animal studies
Multimodal Biomedical Imaging (BiOS) SPIE Photonics West, San Francisco, CA, USA, January 23-26 2010, pp. 717113-717113-9.
Preprint Abstract
Abstract :
Jin Chen, Vivek Venugopal, and Xavier Intes
Time gated functional diffuse optical tomography based on Monte Carlo
Multimodal Biomedical Imaging (BiOS) SPIE Photonics West, San Francisco, CA, USA, January 22nd 2010.
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Invited talks

Miscellaneous

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