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1.
Anal Chim Acta ; 1322: 343075, 2024 Sep 15.
Article in English | MEDLINE | ID: mdl-39182989

ABSTRACT

BACKGROUND: Spectral intensity drift is a frequent issue in analytical processes, especially in long time excitation scanning for large size metal materials, which can significantly adversely impact the accuracy and stability of analysis results. Spectral intensity drift correction is the process of preprocessing spectral data using mathematical algorithms in order to facilitate the subsequent qualitative and quantitative analysis of spectra, especially in combination with stoichiometric methods. Up to now, spectral intensity drift correction within prolonged excitation has not been reported yet. RESULTS: We propose an intensity drift correction method for element content of large-size samples using the Spark Mapping Analysis for Large Samples (SMALS) technique. By considering the row-by-row and column-by-column mapping modes of the SMALS, this includes curve fitting baseline correction for in-row and in-column correction, as well as total average value correction for inter-row and inter-column correction. The final measurement values are derived by coupling rows with columns. The careful implementation of correction steps can enhance baseline correction performance, effectively reducing measurement errors a drift errors. Application of this method to characterize the cross and longitudinal sections of an oversized steel billet indicates high agreement with composition distribution obtained by micro-beam X-ray fluorescence (µ-XRF). The corrected longitudinal and cross-sectional data also exhibit strong alignment. Comparison of statistical analysis results pre- and post-correction demonstrates significant improvements in the clarity of elements segregation pattern. SIGNIFICANCE: This intensity drift correction method not only enhances the spectral quality but also improves the accuracy and robustness of quantitative and qualitative spectral analysis. This study contributes to establishing a robust foundation for component characterization of large-size metal materials using the SMALS technique. The novel spectral intensity correction method shows theoretical significance and practical value for large-scale, long-duration excitation scanning analysis.

2.
Phys Imaging Radiat Oncol ; 31: 100596, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39104731

ABSTRACT

This work investigates the use of a multi-2D cine magnetic resonance imaging-based comprehensive motion monitoring (CMM) system for the assessment of prostate intrafraction 3D drifts. The data of six healthy volunteers were analyzed and the values of a clinically-relevant registration quality factor metric exported by CMM were presented. Additionally, the CMM-derived prostate motion was compared to a 3D-based reference and the 2D-3D tracking agreement was reported. Due to the low quality of SI motion tracking (often > 2 mm tracking mismatch between anatomical planes) we conclude that further improvements are desirable prior to clinical introduction of CMM for prostate drift corrections.

3.
Phys Imaging Radiat Oncol ; 30: 100580, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38707627

ABSTRACT

Background and purpose: MRI-guided online adaptive treatments can account for interfractional variations, however intrafraction motion reduces treatment accuracy. Intrafraction plan adaptation methods, such as the Intrafraction Drift Correction (IDC) or sub-fractionation, are needed. IDC uses real-time automatic monitoring of the tumor position to initiate plan adaptations by repositioning segments. IDC is a fast adaptation method that occurs only when necessary and this method could enable margin reduction. This research provides a treatment planning evaluation and experimental validation of the IDC. Materials and methods: An in silico treatment planning evaluation was performed for 13 prostate patients mid-treatment without and with intrafraction plan adaptation (IDC and sub-fractionation). The adaptation methods were evaluated using dose volume histogram (DVH) metrics. To experimentally verify IDC a treatment was mimicked whereby a motion phantom containing an EBT3 film moved mid-treatment, followed by repositioning of segments. In addition, the delivered treatment was irradiated on a diode array phantom for plan quality assurance purposes. Results: The planning study showed benefits for using intrafraction adaptation methods relative to no adaptation, where the IDC and sub-fractionation showed consistently improved target coverage with median target coverages of 100.0%. The experimental results verified the IDC with high minimum gamma passing rates of 99.1% and small mean dose deviations of maximum 0.3%. Conclusion: The straightforward and fast IDC technique showed DVH metrics consistent with the sub-fractionation method using segment weight re-optimization for prostate patients. The dosimetric and geometric accuracy was shown for a full IDC workflow using film and diode array dosimetry.

4.
Methods Cell Biol ; 187: 249-292, 2024.
Article in English | MEDLINE | ID: mdl-38705627

ABSTRACT

Cryogenic ultrastructural imaging techniques such as cryo-electron tomography have produced a revolution in how the structure of biological systems is investigated by enabling the determination of structures of protein complexes immersed in a complex biological matrix within vitrified cell and model organisms. However, so far, the portfolio of successes has been mostly limited to highly abundant complexes or to structures that are relatively unambiguous and easy to identify through electron microscopy. In order to realize the full potential of this revolution, researchers would have to be able to pinpoint lower abundance species and obtain functional annotations on the state of objects of interest which would then be correlated to ultrastructural information to build a complete picture of the structure-function relationships underpinning biological processes. Fluorescence imaging at cryogenic conditions has the potential to be able to meet these demands. However, wide-field images acquired at low numeric aperture (NA) using air immersion objective have a low resolving power and cannot provide accurate enough three-dimensional (3D) localization to enable the assignment of functional annotations to individual objects of interest or target sample debulking to ensure the preservation of the structures of interest. It is therefore necessary to develop super-resolved cryo-fluorescence workflows capable of fulfilling this role and enabling new biological discoveries. In this chapter, we present the current state of development of two super-resolution cryogenic fluorescence techniques, superSIL-STORM and astigmatism-based 3D STORM, show their application to a variety of biological systems and discuss their advantages and limitations. We further discuss the future applicability to cryo-CLEM workflows though examples of practical application to the study of membrane protein complexes both in mammalian cells and in Escherichia coli.


Subject(s)
Cryoelectron Microscopy , Cryoelectron Microscopy/methods , Humans , Animals , Imaging, Three-Dimensional/methods , Electron Microscope Tomography/methods , Image Processing, Computer-Assisted/methods , Microscopy, Fluorescence/methods
5.
Sensors (Basel) ; 23(17)2023 Aug 22.
Article in English | MEDLINE | ID: mdl-37687782

ABSTRACT

Electromagnetic induction (EMI) systems are used for mapping the soil's electrical conductivity in near-surface applications. EMI measurements are commonly affected by time-varying external environmental factors, with temperature fluctuations being a big contributing factor. This makes it challenging to obtain stable and reliable data from EMI measurements. To mitigate these temperature drift effects, it is customary to perform a temperature drift calibration of the instrument in a temperature-controlled environment. This involves recording the apparent electrical conductivity (ECa) values at specific temperatures to obtain a look-up table that can subsequently be used for static ECa drift correction. However, static drift correction does not account for the delayed thermal variations of the system components, which affects the accuracy of drift correction. Here, a drift correction approach is presented that accounts for delayed thermal variations of EMI system components using two low-pass filters (LPF). Scenarios with uniform and non-uniform temperature distributions in the measurement device are both considered. The approach is developed using a total of 15 measurements with a custom-made EMI device in a wide range of temperature conditions ranging from 10 °C to 50 °C. The EMI device is equipped with eight temperature sensors spread across the device that simultaneously measure the internal ambient temperature during measurements. To parameterize the proposed correction approach, a global optimization algorithm called Shuffled Complex Evolution (SCE-UA) was used for efficient estimation of the calibration parameters. Using the presented drift model to perform corrections for each individual measurement resulted in a root mean square error (RMSE) of <1 mSm-1 for all 15 measurements. This shows that the drift model can properly describe the drift of the measurement device. Performing a drift correction simultaneously for all datasets resulted in a RMSE <1.2 mSm-1, which is considerably lower than the RMSE values of up to 4.5 mSm-1 obtained when using only a single LPF to perform drift corrections. This shows that the presented drift correction method based on two LPFs is more appropriate and effective for mitigating temperature drift effects.

6.
Sensors (Basel) ; 23(13)2023 Jul 05.
Article in English | MEDLINE | ID: mdl-37448006

ABSTRACT

This paper verified through experiments that change in ambient temperature are the main cause of dark output noise drift. Additionally, the impact of dark output noise drift in fiber optic spectrometers on emissivity measurements has been investigated in this work. Based on an improved fiber optic spectrometer, two methods were proposed for characterizing and correcting the dark output noise offset in fiber optic spectrometers: the mean correction scheme and the linear fitting correction scheme. Compared to the mean correction scheme, the linear fitting correction scheme is more effective in solving the problem of dark output noise drift. When the wavelength is greater than 1600 nm, the calibration relative error of silicon carbide (SIC) emissivity is less than 0.8% by the mean correction scheme, while the calibration relative error of silicon carbide emissivity is less than 0.62% by the linear fitting correction scheme. This work solves the problem of dark output noise drift in prolonged measurement based on fiber optic spectrometers, improving the accuracy and reliability of emissivity and quantitative radiation measurement.


Subject(s)
Fiber Optic Technology , Reproducibility of Results
7.
Sensors (Basel) ; 23(14)2023 Jul 19.
Article in English | MEDLINE | ID: mdl-37514828

ABSTRACT

The use of equipment such as oscilloscopes, high-speed cameras or acoustic sensors is quite common to measure detonation times from surface connectors and detonators. However, these solutions are expensive and, sometimes, not adequate to use in field conditions, such as mining or civil works. In this regard, a low-cost portable device is designed and tested using the Arduino platform, achieving a simple, robust and precise system to carry out field measurements. This study describes the characteristics and working principles of the designed device, as well as the verifications carried out to check the accuracy of the Arduino ceramic oscillator. Additionally, a field test was carried out using 100 actual detonators and surface connectors to verify the correct operation of the designed equipment. We have designed a device, and a methodology, to measure detonation instants with a minimum accuracy of 0.1 ms, being sufficient to carry out subsequent studies of detonation time dispersion for non-electric detonators.

8.
Magn Reson Med ; 90(4): 1271-1281, 2023 10.
Article in English | MEDLINE | ID: mdl-37332203

ABSTRACT

PURPOSE: Frequency drift correction is an important postprocessing step in MRS that yields improvements in spectral quality and metabolite quantification. Although routinely applied in single-voxel MRS, drift correction is much more challenging in MRSI due to the presence of phase-encoding gradients. Thus, separately acquired navigator scans are normally required for drift estimation. In this work, we demonstrate the use of self-navigating rosette MRSI trajectories combined with time-domain spectral registration to enable retrospective frequency drift corrections without the need for separately acquired navigator echoes. METHODS: A rosette MRSI sequence was implemented to acquire data from the brains of 5 healthy volunteers. FIDs from the center of k-space ( k = 0 $$ k=0 $$ FIDs) were isolated from each shot of the rosette acquisition, and time-domain spectral registration was used to estimate the frequency offset of each k = 0 $$ k=0 $$ FID relative to a reference scan (the first k = 0 $$ k=0 $$ FID in the series). The estimated frequency offsets were then used to apply corrections throughout k $$ k $$ -space. Improvements in spectral quality were assessed before and after drift correction. RESULTS: Spectral registration resulted in significant improvements in signal-to-noise ratio (12.9%) and spectral linewidths (18.5%). Metabolite quantification was performed using LCModel, and the average Cramer-Rao lower bounds uncertainty estimates were reduced by 5.0% for all metabolites, following field drift correction. CONCLUSION: This study demonstrated the use of self-navigating rosette MRSI trajectories to retrospectively correct frequency drift errors in in vivo MRSI data. This correction yields meaningful improvements in spectral quality.


Subject(s)
Brain , Magnetic Resonance Imaging , Humans , Magnetic Resonance Spectroscopy/methods , Retrospective Studies , Brain/diagnostic imaging , Brain/metabolism , Signal-To-Noise Ratio , Healthy Volunteers , Magnetic Resonance Imaging/methods
9.
J Cell Sci ; 136(4)2023 02 15.
Article in English | MEDLINE | ID: mdl-36727532

ABSTRACT

Unwanted sample drift is a common issue that plagues microscopy experiments, preventing accurate temporal visualization and quantification of biological processes. Although multiple methods and tools exist to correct images post acquisition, performing drift correction of three-dimensional (3D) videos using open-source solutions remains challenging and time consuming. Here, we present a new tool developed for ImageJ or Fiji called Fast4DReg that can quickly correct axial and lateral drift in 3D video-microscopy datasets. Fast4DReg works by creating intensity projections along multiple axes and estimating the drift between frames using two-dimensional cross-correlations. Using synthetic and acquired datasets, we demonstrate that Fast4DReg can perform better than other state-of-the-art open-source drift-correction tools and significantly outperforms them in speed. We also demonstrate that Fast4DReg can be used to register misaligned channels in 3D using either calibration slides or misaligned images directly. Altogether, Fast4DReg provides a quick and easy-to-use method to correct 3D imaging data before further visualization and analysis.


Subject(s)
Imaging, Three-Dimensional , Microscopy , Imaging, Three-Dimensional/methods , Microscopy, Video
10.
Magn Reson Imaging ; 96: 126-134, 2023 02.
Article in English | MEDLINE | ID: mdl-36496098

ABSTRACT

Real-time temperature monitoring is critical to the success of thermally ablative therapies. This work validates a 3D thermometry sequence with k-space field drift correction designed for use in magnetic resonance-guided focused ultrasound treatments for breast cancer. Fiberoptic probes were embedded in tissue-mimicking phantoms, and temperature change measurements from the probes were compared with the magnetic resonance temperature imaging measurements following heating with focused ultrasound. Precision and accuracy of measurements were also evaluated in free-breathing healthy volunteers (N = 3) under a non-heating condition. MR temperature measurements agreed closely with those of fiberoptic probes, with a 95% confidence interval of measurement difference from -2.0 °C to 1.4 °C. Field drift-corrected measurements in vivo had a precision of 1.1 ± 0.7 °C and were accurate within 1.3 ± 0.9 °C across the three volunteers. The field drift correction method improved precision and accuracy by an average of 46 and 42%, respectively, when compared to the uncorrected data. This temperature imaging sequence can provide accurate measurements of temperature change in aqueous tissues in the breast and support the use of this sequence in clinical investigations of focused ultrasound treatments for breast cancer.


Subject(s)
Breast Neoplasms , High-Intensity Focused Ultrasound Ablation , Thermometry , Humans , Female , Temperature , Magnetic Resonance Imaging/methods , Breast/diagnostic imaging , Thermometry/methods , High-Intensity Focused Ultrasound Ablation/methods , Phantoms, Imaging , Breast Neoplasms/diagnostic imaging , Breast Neoplasms/therapy
11.
J Chromatogr A ; 1687: 463700, 2023 Jan 04.
Article in English | MEDLINE | ID: mdl-36508769

ABSTRACT

In untargeted liquid chromatography‒mass spectrometry (LC‒MS) metabolomics studies, data preprocessing and metabolic pathway recognition are crucial for screening important pathways that are disturbed by diseases or restored by drugs. Here, we collected high-resolution mass spectrometry data of serum samples from 221 coronary heart disease (CHD) patients under two different chromatographic columns (BEH amide and C18 column) and evaluated the three commonly used software programs (XCMS, Progenesis QI, MarkerView) from four aspects (including signal drift, peak number, metabolite annotation and metabolic pathway enrichment). The results showed that the data preprocessed by the three software programs have different degrees of signal drift, but the StatTarget could improve the data quality to meet the data analysis requirement after correction. In addition, XCMS surpassed other software in detection of real chromatographic peaks and Progenesis QI was the best performer in terms of the number of metabolite annotation. XCMS and Progenesis QI showed different performance in pathway enrichment. However, metabolic pathways based on the combination of XCMS and Progenesis QI had a high coincidence with Progenesis QI. In addition, we also reported that C18 and amide columns were highly complementary and have great potential for cooperation in the context of metabolic pathways. In this study, the effects of different chromatographic columns and software pretreatments on metabolomics data were evaluated based on clinical large cohort samples, which will provide a reference for the metabolomics of clinical samples and guide subsequent mechanistic research.


Subject(s)
Metabolomics , Software , Humans , Mass Spectrometry/methods , Metabolomics/methods , Amides , Metabolic Networks and Pathways
12.
Beilstein J Nanotechnol ; 14: 1225-1237, 2023.
Article in English | MEDLINE | ID: mdl-38170148

ABSTRACT

Scanning probe microscopy (SPM) techniques are widely used to study the structure and properties of surfaces and interfaces across a variety of disciplines in chemistry and physics. One of the major artifacts in SPM is (thermal) drift, an unintended movement between sample and probe, which causes a distortion of the recorded SPM data. Literature holds a multitude of strategies to compensate for drift during the measurement (online drift correction) or afterwards (offline drift correction). With the currently available software tools, however, offline drift correction of SPM data is often a tedious and time-consuming task. This is particularly disadvantageous when analyzing long image series. Here, we present unDrift, an easy-to-use scientific software for fast and reliable drift correction of SPM images. unDrift provides three different algorithms to determine the drift velocity based on two consecutive SPM images. All algorithms can drift-correct the input data without any additional reference. The first semi-automatic drift correction algorithm analyzes the different distortion of periodic structures in two consecutive up and down (down and up) images, which enables unDrift to correct SPM images without stationary features or overlapping scan areas. The other two algorithms determine the drift velocity from the apparent movement of stationary features either by automatic evaluation of the cross-correlation image or based on positions identified manually by the user. We demonstrate the performance and reliability of unDrift using three challenging examples, namely images distorted by a very high drift velocity, only partly usable images, and images exhibiting an overall weak contrast. Moreover, we show that the semi-automatic analysis of periodic images can be applied to a long series containing hundreds of images measured at the calcite-water interface.

13.
Sensors (Basel) ; 22(9)2022 Apr 26.
Article in English | MEDLINE | ID: mdl-35590991

ABSTRACT

For decades, Metal oxide (MOX) gas sensors have been commercially available and used in various applications such as the Smart City, gas monitoring, and safety due to advantages such as high sensitivity, a high detection range, fast reaction time, and cost-effectiveness. However, several factors affect the sensing ability of MOX gas sensors. This article presents the results of a study on the cross-sensitivity of MOX gas sensors toward ambient temperature and humidity. A gas sensor array consisting of temperature and humidity sensors and four different MOX gas sensors (MiCS-5524, GM-402B, GM-502B, and MiCS-6814) was developed. The sensors were subjected to various relative gas concentrations, temperatures (from 16 °C to 30 °C), and humidity levels (from 75% to 45%), representing a typical indoor environment. The results proved that the gas sensor responses were significantly affected by the temperature and humidity. The increased temperature and humidity levels led to a decreased response for all sensors, except for MiCS-6814, which showed the opposite response. Hence, this work proposed regression models for each sensor, which can correct the gas sensor response drift caused by the ambient temperature and humidity variations. The models were validated, and the standard deviations of the corrected sensor response were found to be 1.66 kΩ, 13.17 kΩ, 29.67 kΩ, and 0.12 kΩ, respectively. These values are much smaller compared to the raw sensor response (i.e., 18.22, 24.33 kΩ, 95.18 kΩ, and 2.99 kΩ), indicating that the model provided a more stable output and minimised the drift. Overall, the results also proved that the models can be used for MOX gas sensors employed in the training process, as well as for other sets of gas sensors.


Subject(s)
Oxides , Humidity , Temperature
14.
Sensors (Basel) ; 22(10)2022 May 20.
Article in English | MEDLINE | ID: mdl-35632291

ABSTRACT

Data measured using electromagnetic induction (EMI) systems are known to be susceptible to measurement influences associated with time-varying external ambient factors. Temperature variation is one of the most prominent factors causing drift in EMI data, leading to non-reproducible measurement results. Typical approaches to mitigate drift effects in EMI instruments rely on a temperature drift calibration, where the instrument is heated up to specific temperatures in a controlled environment and the observed drift is determined to derive a static thermal apparent electrical conductivity (ECa) drift correction. In this study, a novel correction method is presented that models the dynamic characteristics of drift using a low-pass filter (LPF) and uses it for correction. The method is developed and tested using a customized EMI device with an intercoil spacing of 1.2 m, optimized for low drift and equipped with ten temperature sensors that simultaneously measure the internal ambient temperature across the device. The device is used to perform outdoor calibration measurements over a period of 16 days for a wide range of temperatures. The measured temperature-dependent ECa drift of the system without corrections is approximately 2.27 mSm-1K-1, with a standard deviation (std) of only 30 µSm-1K-1 for a temperature variation of around 30 K. The use of the novel correction method reduces the overall root mean square error (RMSE) for all datasets from 15.7 mSm-1 to a value of only 0.48 mSm-1. In comparison, a method using a purely static characterization of drift could only reduce the error to an RMSE of 1.97 mSm-1. The results show that modeling the dynamic thermal characteristics of the drift helps to improve the accuracy by a factor of four compared to a purely static characterization. It is concluded that the modeling of the dynamic thermal characteristics of EMI systems is relevant for improved drift correction.

15.
Phys Med Biol ; 67(4)2022 02 18.
Article in English | MEDLINE | ID: mdl-35086077

ABSTRACT

Motion tracking techniques can revise the bias arising from respiration-caused motion in radiation therapy. Tracking key structures accurately and at a real-time speed is necessary for effective motion tracking. In this work, we propose a fusion Siamese network with drift correction for target tracking in ultrasound sequences. Specifically, the network fuses four response maps generated by the cross-correlation between convolution layers at different resolutions to reduce up-sampling error. A correction strategy combining local structural similarity and target trajectory is proposed to revise the target drift predicted by the network. Moreover, a coarse-to-fine strategy is proposed to train the network with a limited number of annotated images, in which an augmented dataset is generated by corner points to learn network features with high generalizability. The proposed method is evaluated on the basis of the public dataset of the MICCAI 2015 Challenge on Liver UltraSound Tracking (CLUST) and our ultrasound image dataset, which is provided by the Chinese People's Liberation Army General Hospital (CPLAGH). A tracking error of 0.80 ± 1.16 mm is observed for 85 targets across 39 ultrasound sequences in the CLUST dataset. A tracking error of 0.61 ± 0.36 mm is observed for 20 targets across 10 ultrasound sequences in the CPLAGH dataset. The effectiveness of the proposed fusion and correction strategies is verified via two ablation experiments. Overall, the experimental results demonstrate the effectiveness of the proposed fusion Siamese network with drift correction and reveal its potential in clinical practice.


Subject(s)
Respiration , Humans , Motion , Ultrasonography/methods
16.
Appl Radiat Isot ; 181: 110069, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34959043

ABSTRACT

Gamma-ray detection systems are exposed to extreme environments during in situ measurements and the NaI(TI)-detectors in these systems are frequently subjected to significant temperature fluctuations. Several elements within these detectors are sensitive to temperature deviations, which ultimately causes a drift in gamma-ray spectra. This study aimed to determine the relationship between temperature deviation and spectrum drift and found a linear relationship over a wide range of energies. It was found that an increase in the detector temperature shifts the gamma-ray spectrum to lower channels, whereas a decrease in the detector temperature shifts the spectrum to higher channels. Using this information, a novel drift correction method based on the Gaussian distribution of the 1460 keV gamma-peak of 40K was developed. Dividing the peak into five regions of interest (ROI), a weighted gain correction factor is calculated based on the comparative skewness of the measured data and the sensitivity of the drift. The detector gain is then adjusted by the same factor to correct the drift in gamma-spectrum. This method was first tested in a simulated in situ environment, followed by in situ measurements along a beach. As expected, the gain adjustments followed the trend in detector temperature. The corrected counts in each of the five bins also presented good results and a close fit to the Gaussian distribution.

17.
Behav Res Methods ; 54(5): 2545-2564, 2022 10.
Article in English | MEDLINE | ID: mdl-34918232

ABSTRACT

Interest in applications for the simultaneous acquisition of data from different devices is growing. In neuroscience for example, co-registration complements and overcomes some of the shortcomings of individual methods. However, precise synchronization of the different data streams involved is required before joint data analysis. Our article presents and evaluates a synchronization method which maximizes the alignment of information across time. Synchronization through common triggers is widely used in all existing methods, because it is very simple and effective. However, this solution has been found to fail in certain practical situations, namely for the spurious detection of triggers and/or when the timestamps of triggers sampled by each acquisition device are not jointly distributed linearly for the entire duration of an experiment. We propose two additional mechanisms, the "Longest Common Subsequence" algorithm and a piecewise linear regression, in order to overcome the limitations of the classical method of synchronizing common triggers. The proposed synchronization method was evaluated using both real and artificial data. Co-registrations of electroencephalographic signals (EEG) and eye movements were used for real data. We compared the effectiveness of our method to another open source method implemented using EYE-EEG toolbox. Overall, we show that our method, implemented in C++ as a DOS application, is very fast, robust and fully automatic.


Subject(s)
Electroencephalography , Eye Movements , Humans , Electroencephalography/methods , Algorithms
18.
Sensors (Basel) ; 21(24)2021 Dec 20.
Article in English | MEDLINE | ID: mdl-34960584

ABSTRACT

Thermal drift of nano-computed tomography (CT) adversely affects the accurate reconstruction of objects. However, feature-based reference scan correction methods are sometimes unstable for images with similar texture and low contrast. In this study, based on the geometric position of features and the structural similarity (SSIM) of projections, a rough-to-refined rigid alignment method is proposed to align the projection. Using the proposed method, the thermal drift artifacts in reconstructed slices are reduced. Firstly, the initial features are obtained by speeded up robust features (SURF). Then, the outliers are roughly eliminated by the geometric position of global features. The features are refined by the SSIM between the main and reference projections. Subsequently, the SSIM between the neighborhood images of features are used to relocate the features. Finally, the new features are used to align the projections. The two-dimensional (2D) transmission imaging experiments reveal that the proposed method provides more accurate and robust results than the random sample consensus (RANSAC) and locality preserving matching (LPM) methods. For three-dimensional (3D) imaging correction, the proposed method is compared with the commonly used enhanced correlation coefficient (ECC) method and single-step discrete Fourier transform (DFT) algorithm. The results reveal that proposed method can retain the details more faithfully.

19.
Bio Protoc ; 11(13): e4074, 2021 Jul 05.
Article in English | MEDLINE | ID: mdl-34327271

ABSTRACT

The data quality of high-resolution imaging can be markedly improved with active stabilization, which is based on feedback loops within the microscope that maintain the sample in the same location throughout the experiment. The purpose is to provide a highly accurate focus lock, therefore eliminating drift and improving localization precision. Here, we describe a step-by-step protocol for building a total internal reflection microscope combined with the feedback loops necessary for sample and detection stabilization, which we routinely use in single-molecule localization microscopy (SMLM). The performance of the final microscope with feedback loops, called feedback SMLM, has previously been described. We demonstrate how to build a replica of our system and include a list of the necessary optical components, tips, and an alignment strategy.

20.
Talanta ; 233: 122511, 2021 Oct 01.
Article in English | MEDLINE | ID: mdl-34215126

ABSTRACT

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become the most versatile analytical tool for profiling small-molecule compounds and increasingly been applied in many fields. Nevertheless, LC-MS based quantification still face some challenges, such as signal drift in LC-MS, which may affect the validity of the obtained data and lead to misinterpretation of biological results. Here, we established a calibration method known as "RIM" to compensate the signal drift of LC-MS. To this end, a mixture of d4-2-dimethylaminoethylamine (d4-DMED)-coded normal fatty acids (C5-C23) was used as calibrants to construct RIM calibration. With the addition of calibrants, not only the MS signal drift, but also the mass accuracy and LC retention time can be calibrated, thereby improving the reliability of quantitative data. The effectiveness of RIM was carefully validated using a human serum extract spiked with 34 standards and then RIM was applied for rat brain untargeted metabolome research. In addition, to expand the functionality and flexibility of RIM for data handling, we generated a MATLAB-based RIM program, which implements the above concepts and allows automatic data process. Taken together, the proposed RIM method has potential application in large-scale quantitative study of complex samples.


Subject(s)
Fatty Acids , Metabolome , Chromatography, Liquid , Mass Spectrometry , Reproducibility of Results
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