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Light-microscopy methods in C. elegans research
摘要： Ever since Caenorhabditis elegans was introduced as a model system it has been tightly linked to microscopy, which has led to significant advances in understanding biology over the last decades. Developing new technologies therefore is an essential part in the endeavor to gain further mechanistic insights into developmental biology. This review will discuss state-of-the-art developments in quantitative light microscopy in the context of C. elegans research as well as the impact these technologies have on the field. We will highlight future developments that currently promise to revolutionize biological research by combining sequencing-based single-cell technologies with high-resolution quantitative imaging.
关键词： quantitative imaging,light microscopy,developmental biology,single-cell technologies,C. elegans
更新于2025-09-23 15:21:21
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Special Section Guest Editorial: Quantitative Imaging and the Pioneering Efforts of Laurence P. Clarke
摘要： Quantitative imaging is growing in popularity and clinical utility, and this special section of the Journal of Medical Imaging features articles that present results of this method across medical imaging modalities and applications. Quantitative imaging is the science of extracting numeric information from images to measure or predict a patient’s health. Larry Clarke was an early and enthusiastic champion of quantitative methods in medical imaging, and the fullness and diversity of this issue stand as a tribute to his dedication to the field. Sadly, Larry passed away in April 2016 before many aspects of his vision for quantitative imaging could be realized.
关键词： National Cancer Institute,Cancer Imaging Program,Medical Imaging,Quantitative Imaging,Laurence P. Clarke
更新于2025-09-23 15:21:01
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NanoJ: a high-performance open-source super-resolution microscopy toolbox
摘要： Super-resolution microscopy has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for super-resolution microscopy designed to combine high performance and ease of use. We named it NanoJ - a reference to the popular ImageJ software it was developed for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJSQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.
关键词： Virus,Vaccinia,Archaea,Quantitative imaging,Sulfolobus acidocaldarius,Super-resolution microscopy,Fluidics,Modelling,Resolution,Image quality assessment,Pox,Image analysis,ImageJ,Fiji
更新于2025-09-19 17:15:36
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Laser speckle imaging of flowing blood: A numerical study
摘要： Laser speckle imaging (LSI) can be used to study dynamic processes in turbid media, such as blood flow. However, it is presently still challenging to obtain meaningful quantitative information from speckle, mainly because speckle is the interferometric summation of multiply scattered light. Consequently, speckle represents a convolution of the local dynamics of the medium. In this paper, we present a computational model for simulating the LSI process, which we aim to use for improving our understanding of the underlying physics. Thereby reliable methods for extracting meaningful information from speckle can be developed. To validate our code, we apply it to a case study resembling blood flow: a cylindrical fluid flow geometry seeded with small spherical particles and modulated with a heartbeat signal. From the simulated speckle pattern, we successfully retrieve the main frequency modes of the original heartbeat signal. By comparing Poiseuille flow to plug flow, we show that speckle boiling causes a small amount of uniform spectral noise. Our results indicate that our computational model is capable of simulating LSI and will therefore be useful in future studies for further developing LSI as a quantitative imaging tool.
关键词： speckle boiling,Laser speckle imaging,computational model,quantitative imaging,blood flow
更新于2025-09-16 10:30:52
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Fourier transforms for fast and quantitative Laser Speckle Imaging
摘要： Laser speckle imaging is a powerful imaging technique that visualizes microscopic motion within turbid materials. At current two methods are widely used to analyze speckle data: one is fast but qualitative, the other quantitative but computationally expensive. We have developed a new processing algorithm based on the fast fourier transform, which converts raw speckle patterns into maps of microscopic motion and is both fast and quantitative, providing a dynamnic spectrum of the material over a frequency range spanning several decades. in this article we show how to apply this algorithm and how to measure a diffusion coefficient with it. We show that this method is quantitative and several orders of magnitude faster than the existing quantitative method. finally we harness the potential of this new approach by constructing a portable laser speckle imaging setup that performs quantitative data processing in real-time on a tablet.
关键词： Fast Fourier Transform,Real-time Analysis,Quantitative Imaging,Laser Speckle Imaging,Microscopic Motion
更新于2025-09-12 10:27:22
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The effect of different image reconstruction techniques on pre-clinical quantitative imaging and dual-energy CT
摘要： To analyse the effect of different image reconstruction techniques on image quality and dual energy CT (DECT) imaging metrics. A software platform for pre-clinical cone beam CT X-ray image reconstruction was built using the open-source reconstruction toolkit. Pre-processed projections were reconstructed with filtered back-projection and iterative algorithms, namely Feldkamp, Davis, and Kress (FDK), Iterative FDK, simultaneous algebraic reconstruction technique (SART), simultaneous iterative reconstruction technique and conjugate gradient. Imaging metrics were quantitatively assessed, using a quality assurance phantom, and DECT analysis was performed to determine the influence of each reconstruction technique on the relative electron density (ρe) and effective atomic number (Zeff) values. Iterative reconstruction had favourable results for the DECT analysis: a significantly smaller spread for each material in the ρe-Zeff space and lower Zeff and ρe residuals (on average 24 and 25% lower, respectively). In terms of image quality assurance, the techniques FDK, Iterative FDK and SART provided acceptable results. The three reconstruction methods showed similar geometric accuracy, uniformity and CT number results. The technique SART had a contrast-to-noise ratio up to 76% higher for solid water and twice as high for Teflon, but resolution was up to 28% lower when compared to the other two techniques. Advanced image reconstruction can be beneficial, but the benefit is small, and calculation times may be unacceptable with current technology. The use of targeted and downscaled reconstruction grids, larger, yet practicable, pixel sizes and GPU are recommended. An iterative CBCT reconstruction platform was build using RTK.
关键词： image reconstruction,iterative reconstruction,quantitative imaging,dual-energy CT,pre-clinical imaging
更新于2025-09-11 14:15:04
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Radiobiological Modeling Based on 18F-Fluorodeoxyglucose Positron Emission Tomography Data for Esophageal Cancer
摘要： Background: We investigated the relationship of standardized uptake values (SUVs) to radiobiological parameters, such a 25 s tumor control probability (TCP), to allow for quantitative prediction of tumor response based on SUVs from 18F fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) before and after treatment for esophageal cancer. Methods: We analyzed data from 20 esophageal cancer patients treated with chemoradiotherapy (CRT) followed by surgery. Tumor pathologic response to CRT was assessed in surgical specimens. Patients underwent 18F-FDG PET imaging before and after CRT. Rigid image registration was performed between both images. Because TCP in a heterogeneous tumor is a function of average cell survival, we modeled TCP as a function of <SUVR>, a possible surrogate for average cell survival (<SUVR>=<SUVafter/SUVbefore>). TCP was represented by a sigmoid function with two parameters: SUVR50, the <SUVR> at which TCP=0.5, and γ50, the slope of the curve at SUVR50. The two parameters and their confidence intervals (CIs) were estimated using the maximum-likelihood method. The correlation between SUV before CRT and SUV change <SUVbefore – SUVafter> was also studied. Results: A TCP model as a function of SUV before and after treatment was developed for esophageal cancer patients. The maximum-likelihood estimate of SUVR50 was 0.47 (90% CI, 0.30-0.61) and for γ50was 1.62 (90% CI, 0-4.2). High initial SUV and larger metabolic response (larger <SUVbefore –SUVafter>) were correlated, and this correlation was stronger among responders. Conclusions: Our TCP model indicates that <SUVafter/SUVbefore> is a possible surrogate for cell survival in esophageal cancer patients. Although CIs are large as a result of the small patient sample, parameters for a TCP curve can be derived and an individualized TCP can be calculated for future patients. Initial SUV does not predict response, whereas a correlation is found between surrogates for initial tumor burden and cell kill during therapy.
关键词： Quantitative imaging,Esophageal cancer,18F-FDG PET/CT,Tumor response,Radiation therapy
更新于2025-09-09 09:28:46
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Robust beam hardening artifacts reduction for computed tomography (CT) using spectrum modeling
摘要： The aim of this study was to develop a fast and accurate beam hardening correction method by modeling physical interactions between X-ray photons and materials for computed tomography (CT) imaging. The nonlinear attenuation process of the X-ray projection was modeled by reprojecting a template image with the estimated polychromatic spectrum. By adding the scaled difference of the monochromatic reprojection data and the polychromatic reprojection to the raw projection data, the raw projection data was mapped into the corresponding monochromatic projection data, which was used to reconstruct the beam hardening artifacts corrected images. The algorithm can also be implemented in image-domain which takes the uncorrected image volume as input when there is an adequate model of the spectrum. In this case, the scaled difference was reconstructed to yield a set of artifacts images which can be added directly to the uncorrected images. Numerical simulations, experimental phantom data, and animal data which were acquired on a modern diagnostic CT scanner (Discovery CT750 HD, GE Healthcare, WI, USA), and a modern C-Arm CT scanner (Artis Zee, Siemens Healthcare, Forchheim, Germany), respectively, were used to evaluate the proposed method. The results show the proposed method significantly reduced both cupping and streak artifacts, and successfully recovered the Housfield Units (HU) accuracy. Extensive studies suggest the proposed model-based method successfully corrects the beam hardening artifacts. This work is practically useful and is promising to be applied to commercial products.
关键词： Computed tomography,quantitative imaging,spectrum modeling,polychromatic forward projection,beam hardening correction
更新于2025-09-09 09:28:46
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THE FACTORIZATION METHOD FOR VIRTUAL EXPERIMENTS BASED QUANTITATIVE INVERSE SCATTERING
摘要： The concept of virtual experiments is based on the idea of solving the inverse scattering problem by processing a suitable recombination of the available data, instead of those arising from the measurements. By properly designing such experiments (and without additional measurements), it is possible to enforce some peculiar ?eld’s or contrast source’s properties, which can be helpful to perform the inversion in a more simple and reliable way. In this paper, we show that the factorization method can be used as a tool to design the virtual experiments. In doing so, we also provide, for the ?rst time, an insight into its physical meaning. As an example, we exploit the virtual experiments designed via FM as the backbone of a linearized inversion approach for quantitative imaging of non-weak targets.
关键词： Quantitative Imaging,Inverse Scattering,Factorization Method,Virtual Experiments
更新于2025-09-09 09:28:46
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Multi-probe ptychographic iterative engine method
摘要： As a lensfree imaging technique, ptychographic iterative engine (PIE) can provide quantitative amplitude and phase distributions of samples in an extremely large field of view but without aberrations. However, relying on the single pinhole scanning, PIE is time-consuming in both diffraction recording and sample reconstruction, thus limiting its potentiality in dynamic imaging applications. In order to reduce the diffraction captures and increase its processing efficiency, we design the multi-probe PIE, in which a pinhole array is adopted instead of traditionally used single pinhole, thus diffractions at different positions can be captured simultaneously. Moreover, the multi-probe PIE reconstruction algorithm is also implemented to further accelerate the sample reconstruction speed. Proved by experiments, less than 10 s is required for diffraction recording for a large field of view of ~150 mm2, and combining with the modified multi-probe PIE reconstruction algorithm, high-resolution quantitative sample information can be extracted accurately with much faster speed compared to traditional PIE reconstruction algorithm. It is believed the proposed multi-probe PIE can be future applied in dynamic imaging.
关键词： Quantitative imaging,Ptychographic iterative engine,Digital micro-mirror device
更新于2025-09-04 15:30:14