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Attention-based CT scan interpolation for lesion segmentation of colorectal liver metastases

Attention-based CT scan interpolation for lesion segmentatio...

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Medical imaging 2023: biomedical applications in molecular, structural, and functional imaging

作者： Hamghalam, Mohammad Do, Richard K. G. Simpson, Amber L. School of Computing Queen's University KingstonON Canada Department of Electrical Engineering Qazvin Branch Islamic Azad University Qazvin Iran Department of Radiology Memorial Sloan Kettering Cancer Center New YorkNY United States Department of Biomedical and Molecular Sciences Queen's University KingstonON Canada

ISBN: (纸本)9781510660410

Small liver lesions common to colorectal liver metastases (CRLMs) are challenging for convolutional neural network (CNN) segmentation models, especially when we have a wide range of slice thicknesses in the computed tomography (CT) scans. Slice thickness of CT images may vary by clinical indication. For example, thinner slices are used for presurgical planning when fine anatomic details of small vessels are required. While keeping the effective radiation dose in patients as low as possible, various slice thicknesses are employed in CRLMs due to their limitations. However, differences in slice thickness across CTs lead to significant performance degradation in CT segmentation models based on CNNs. This paper proposes a novel unsupervised attention-based interpolation model to generate intermediate slices from consecutive triplet slices in CT scans. We integrate segmentation loss during the interpolation model's training to leverage segmentation labels in existing slices to generate middle ones. Unlike common interpolation techniques in CT volumes, our model highlights the regions of interest (liver and lesions) inside the abdominal CT scans in the interpolated slice. Moreover, our model's outputs are consistent with the original input slices while increasing the segmentation performance in two cutting-edge 3D segmentation pipelines. We tested the proposed model on the CRLM dataset to upsample subjects with thick slices and create isotropic volume for our segmentation model. The produced isotropic dataset increases the Dice score in the segmentation of lesions and outperforms other interpolation approaches in terms of interpolation metrics. © COPYRIGHT spie. Downloading of the abstract is permitted for personal use only.

关键词： Interpolation

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Combining Optical Coherence Tomography with Fluorescence molecular imaging: Towards Simultaneous Morphology and molecular imaging

Combining Optical Coherence Tomography with Fluorescence Mol...

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conference on Advanced biomedical and Clinical Diagnostic Systems VII

作者： Yuan, Shuai Lai, Michael Roney, Celeste A. Jiang, James Li, Qian Ma, Hongzhou Cable, Alex Summers, Ronald M. Chen, Yu Univ Maryland Fischell Dept Bioengn College Pk MD 20742 USA NIH Clin Ctr Dept Radiol & Imaging Sci Bethesda MD 20892 USA Thorlabs Inc Newton NJ 07860 USA

ISBN: (纸本)9780819474155

Optical coherence tomography (OCT) provides high-resolution, cross-sectional imaging of tissue microstructure in situ and in real-time, while fluorescence molecular imaging (FMI) enables the visualization of basic molecular processes. There are great interests in combining these two modalities so that the tissue's structural and molecular information can be obtained simultaneously. This could greatly benefit biomedical applications such as detecting early diseases and monitoring therapeutic interventions. In this research, a new optical system that combines OCT and FMI was developed. The system demonstrated that it could co-register en face OCT and FMI images with a 2.4 x 2.4 mm field of view. The transverse resolutions of OCT and FMI of the system are both 10 mu m. Capillary tubes filled with Cy 5.5 fluorescent dye in different concentrations (750nM to 24 mu M) under a scattering medium (1% - 2% intralipid) are used as the phantom. En face OCT images of the phantoms were obtained and successfully co-registered with FMI images that were acquired simultaneously. A linear relationship between FMI intensity and dye concentration was observed. The relationship between FMI intensity and target fluorescence tube depth measured by OCT images was also observed and compared with theoretical modeling. This relationship could help in correcting reconstructed dye concentration. imaging of colon polyps of APC(min) mouse model is presented as an example of biological applications of this co-registered OCT/FMI system. In conclusion, a co-registering OCT and FMI imaging system has been demonstrated. The system enables simultaneous visualization of tissue morphology and molecular information at high resolutions over a 2-3 mm field-of-view.

关键词： OCT fluorescence molecular imaging colon cancer

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Coherent Nonlinear Optical Microscopy for Acquiring structural Information of Cell Cytoskeleton 9

Coherent Nonlinear Optical Microscopy for Acquiring Structur...

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conference on Nonlinear Optics and applications IX

作者： Sharoukhov, D. Lim, H. CUNY Hunter Coll Dept Phys & Astron New York NY 10065 USA CUNY Grad Ctr New York NY 10065 USA

ISBN: (纸本)9781628416244

Second-harmonic generation (SHG) is a coherent nonlinear optical process occurring in non-centrosymmetric molecules, including microtubule (MT). MT is a cytoskeleton playing many important roles in a variety of cellular processes depending on the cell type, and the conformation is crucial for the function. Here we present the use of SHG process to probe MT cytoskeleton in living neuronal tissue. Polarization-resolved SHG (p-SHG) imaging and the second-order tensor analysis were performed on the retinal nerve fibers in order to probe the structure of MTs in axon. The polar anisotropy of tubulins was determined at the molecular level. The effect of MT-stabilizing drug Taxol was also examined and the induced changes were not detectable by p-SHG. Our results demonstrate SHG as a novel optical method to measure conformational changes of MTs in the native cellular context. The technique could be employed in conjunction with existing atomic-resolution methods of structural biology to improve our understanding of cytoskeleton dynamics in vivo.

关键词： Nonlinear optics biomedical imaging biophysics cytoskeleton

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Assessment of the human trabecular bone structure using Minkowski functionals

Assessment of the human trabecular bone structure using Mink...

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Medical imaging 2009: biomedical applications in molecular, structural, and functional imaging

作者： Monetti, Roberto Bauer, Jan Sidorenko, Irina Müller, Dirk Rummeny, Ernst Matsuura, Maiko Eckstein, Felix Lochmueller, Eva-Maria Zysset, Philippe Räth, Christoph Max-Planck-Institut fuer extraterrestrische Physik Giessenbachstr. 1 85748 Garching Germany Department of Radiology Technische Universitaet Muenchen Ismaninger Str. 22 81675 Munich Germany Department of Anatomy Ludwig-Maximilian-University Pettenkoferstr 11 80336 Munich Germany Institute of Anatomy and Musculoskeletal Research Paracelsus Private Medical University5020 Salzburg Austria Department of Gynecology I Ludwig-Maximilian-University Maistr. 11 80336 Munich Germany Institute for Lightweight Design and Structural Biomechanics Vienna University of Technology Gusshausstr. 27-29 1040 Vienna Austria

ISBN: (纸本)9780819475138

Osteoporosis is bone disease which leads to low bone mass and the deterioration of the bone micro-architecture. *** bone structures are more susceptible to fractures which are the worst complications of osteoporosis. Bone mineral density is considered to be the standard technique for predicting the bone strength and the *** of drug therapy. However, other properties of the bone like the trabecular structure and connectivity may also contribute. Here, we analyze ì-CT tomographic images for a sample of 151 specimens taken from human vertebrae in vitro. Using the local structural characterization of the bone trabecular network given by isotropic and anisotropic scaling indices, we generate structural decompositions of the ì-CT image and quantify the resulting patterns applying topological measures, namely the Minkowski functionals (MF). The values of the MF are then used to assess the biomechanical properties of trabecular bone via a correlation analysis. Biomechanical properties were *** by the maximum compressive strength calculated in an uniaxial compression test. We compare our results with those obtained using standard global histomorphometric parameters and the bone fraction BV/TV . Results obtained using structural decompositions obtained from anisotropic scaling indices were superior to those given by isotropic scaling indices. The highest correlation *** (r = 0.72) was better than those obtained for the standard global histomorphometric parameters and only comparable with the one given by BV/TV. Our results suggest that plate-like and dense column- like structures aligned along the direction of the external force play a relevant role for the prediction of bone strength. © 2009 spie.

关键词： Bone

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Dynamical and structural diagnostics of living tissues using speckle techniques

Dynamical and structural diagnostics of living tissues using...

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conference on Coherence Domain Optical Methods in biomedical Science and Clinical applications IV

作者： Tuchin, VV Zimnykov, DA Gaianzha, EI Ulianov, SS Sinichkin, YP Mishin, AB Chaussky, AA Ryabukho, VP Saratov NG Chernyshevskii State Univ Saratov 410026 Russia

ISBN: (纸本)0819435317

Basing on such fundamental optical phenomena as elastic and quasi-elastic light scattering, diffraction, and interference of optical fields we have designed coherent optical methods offering much promise for biomedical applications. The scope of research includes the development of photon-correlation spectroscopy, speckle-interferometry, coherent micro-topography of living tissues, and study of optical images contrasting due to reduction of scattering properties of surrounding medium using immersion liquids. It was shown that speckle methods can be used as high resolution and high-performance tomographic techniques for imaging of both anatomical (on a micro- and nano-scale) and functional (blood and lymph flow) states of a tissue. Many advantages can be achieved in the field of speckle-polarization effects providing additional selectivity and sensitivity to tissue structure and material anisotropy. Speckle techniques using focused laser beams, including speckle-correlometry, speckle-interferometry, and spatial-domain laser technique, for tissue structure monitoring with a subcellular resolution and in vivo study of changes of velocity of blood and lymph in microvessels were developed. In vivo experimental study of optical and structural properties of such living tissues as skin, impregnated by glycerol and some other ointments were done.

关键词： speckles interferometry scattering,. tissue blood lymph visual acuity

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Multi-modality systems for molecular tomographic imaging

Multi-modality systems for molecular tomographic imaging

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Asia Communications and Photonics conference and Exhibition, ACP 2009

作者： Bai, Jing Li, Mingze Department of Biomedical Engineering School of Medicine Tsinghua University Beijing 100084 China

ISBN: (纸本)9781557528773

Multi-modality imaging, which combines different imaging methods to provide structural, functional and molecular information in one single context, is an important trend in both small animal imaging and clinical research. This presentation introduces some recent advances of multimodality and highlights two systems, FMT-CT and FMT-PET to show their distinct advantages. © 2009 Optical Society of America.

关键词： Clinical research

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Progress in biomedical Optics and imaging - Proceedings of spie

Progress in Biomedical Optics and Imaging - Proceedings of S...

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Medical imaging 2016: biomedical applications in molecular, structural, and functional imaging

ISBN: (纸本)9781510600232

The proceedings contain 94 papers. The topics discussed include: surface displacement based shape analysis of central brain structures in preterm-born children;large-scale Granger causality analysis on resting-state functional MRI;modeling the brain morphology distribution in the general aging population;mutual connectivity analysis (MCA) using generalized radial basis function neural networks for nonlinear functional connectivity network recovery in resting-state functional MRI;non-rigid estimation of cell motion in calcium time-lapse images;automated reconstruction of standing posture panoramas from multi-sector long limb x-ray images;trabecular bone texture classification using wavelet leaders;patellar segmentation from 3d magnetic resonance images using guided recursive ray-tracing for edge pattern detection;intensity-based femoral atlas 2D/3D registration using Levenberg-Marquardt optimisation;examining the neural correlates of depressive and motor symptoms in Parkinson's disease using frequency component analysis (FCA);and detecting altered connectivity patterns in HIV associated neurocognitive impairment using mutual connectivity analysis.

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Cancer Therapy Utilizing molecular Layer Deposition (MLD) and Self-Organized Lightwave Network (SOLNET): Proposal and Theoretical Prediction

Cancer Therapy Utilizing Molecular Layer Deposition (MLD) an...

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conference on Reporters, Markers, Dyes, Nanoparticles, and molecular Probes for biomedical applications IV

作者： Yoshimura, Tetsuzo Yoshino, Chie Sasaki, Koyo Sato, Taishi Seki, Masatoshi Tokyo Univ Technol Hachioji Tokyo 1920982 Japan

ISBN: (纸本)9780819488763

Cancer therapy utilizing molecular Layer Deposition (MLD) and Self-Organized Lightwave Network (SOLNET) is proposed. MLD is a growth method, in which different kinds of molecules are sequentially provided to a substrate to synthesize organic tailored materials with designated molecular arrangements. In cancer therapy, the liquid-phase MLD (LP-MLD) is used with regarding the human body as the MLD chamber and the cancer cells as the substrates. The first proposal is the selective delivery of multi-functional materials with imaging, sensitizing, paramagnetic, light-absorbing agents etc. to cancer cells by LP-MLD. The second proposal is in-situ synthesis of drugs, especially large and toxic ones, at cancer cells by LP-MLD to deliver the drugs deep inside the cancer without attacking normal cells. The third proposal is the SOLNET-assisted laser surgery. After luminescent molecules are adsorbed in cancer cells by LP-MLD, a write beam is introduced from an optical fiber into the area containing cancer cells through photo-induced refractive index increase materials to construct self-aligned optical waveguides of SOLNET, which selectively guides surgery beams to cancer cells. Theoretical predictions and preliminary experimental results are presented.

关键词： molecular layer deposition (MLD) self-organized lightwave network (SOLNET) optical waveguide drug delivery systems cancer therapy laser surgery in-situ synthesis finite difference time domain (FDTD) method

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Progress in biomedical Optics and imaging - Proceedings of spie

Progress in Biomedical Optics and Imaging - Proceedings of S...

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Medical imaging 2018: biomedical applications in molecular, structural, and functional imaging

ISBN: (纸本)9781510616455

The proceedings contain 85 papers. The topics discussed include: classifying Alzheimer's disease using probability distribution distance of fractional anisotropy and trace from diffusion tensor imaging in combination with whole-brain segmentations;brain functional mapping and network connectivity of reconstructed magnetic susceptibility data;alternating segmentation and simulation for contrast adaptive tissue classification;tests of clustering thalamic nuclei based on various dMRI models in the squirrel monkey brain;quantitative dynamic MRI (QdMRI) volumetric analysis of pediatric patients with thoracic insufficiency syndrome;comparing diffusion tensor and spherical harmonic tractography for in utero studies of fetal brain connectivity;investigating directed functional connectivity between the resting state networks of the human brain using mutual connectivity;resilient modular small-world directed brain networks in healthy subjects with large-scale Granger causality analysis of resting-state functional MRI;investigating large-scale granger causality analysis in presence of noise and varying sampling rate;automatic outlier detection using hidden Markov model for cerebellar lobule segmentation;multi-atlas segmentation of the hydrocephalus brain using an adaptive ventricle atlas;toward modeling the effects of regional material properties on the wall stress distribution of abdominal aortic aneurysms;and 3D printed cardiovascular patient specific phantoms used for clinical validation of a CT-derived FFR diagnostic software.

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In-vivo resolution of two near-infrared fluorophores by time-domain diffuse optical imaging

In-vivo resolution of two near-infrared fluorophores by time...

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conference on Genetically Engineered and Optical Probes for biomedical applications IV

作者： Akers, Walter Achilefu, Samuel Washington Univ Sch Med Dept Radiol Opt Radiol Lab St Louis MO 63146 USA

ISBN: (纸本)9780819465627

Fluorescent techniques developed for probing molecular events in vitro have been translated to small animal in-vivo fluorescence imaging using narrow-band, high-power laser sources, fast photon detection electronics and sophisticated image reconstruction algorithms. Targeted near-infrared fluorescent probes are being developed to increase image contrast and functional information collected by the in-vivo optical images. Besides fluorescence intensity, fluorescence lifetime can also be utilized to probe tissue physiology. Fluorescence lifetime, the average time that a fluorophore remains in the excited state, is specific to the molecule and its environment, but not necessarily to its concentration. Therefore, fluorescence lifetime imaging can be used to probe microenvironments within tissues to differentiate, for example, cancer from surrounding tissue by physiological differences. In the current study we demonstrate the ability to distinguish between two molecular probes in mice using fluorescence lifetime while using single excitation and emission wavelengths. Fluorescence detection was accomplished by measuring diffuse emission at 3 mm distance from excitation and raster-scanning whole-body regions of interest using time-correlated single photon counting technique. The resulting temporal point-spread function data was collected for grid points 1.5 min apart. Fluorescence decays were de-convolved to determine measured fluorescence lifetimes by least-squares fit with associated chi-square error values. Relative signal from each fluorophore was then determined for specific tissues including liver, kidney and tumor areas. The results demonstrate that relative biodistributions of individual fluorophores with similar photonic characteristics can be simultaneously monitored in vivo using fluorescence lifetime imaging.

关键词： near-infrared fluorescence lifetime optical imaging mouse cancer cypate bacteriochlorophyll molecular probe

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