High-resolution, broad-spectral-range Raman measurement using a spatial heterodyne spectrometer with separate filters and multi-gratings.

We propose a high-resolution, broad-spectral-range spatial heterodyne Raman spectrometer (SHRS) having separate filters and multi-gratings (SFMG). A prototype of the SFMG-SHRS is built using multi-gratings with four sub-gratings having groove densities of 320, 298, 276, and 254 gr/mm and separate filters with filter bands corresponding to the sub-gratings. We use the SFMG-SHRS to measure the Raman spectra of inorganic and organic compounds with various integration times, laser power, and transparent containers, compare measurements of microplastics with and without the separate filters, and measure mixtures of inorganic powders and organic solutions. The designed SFMG-SHRS makes high-resolution, broad-spectral-range Raman measurements with improved signal-to-noise ratios and visibility of weak Raman peaks even in the presence of fluorescence.

Development of a high-resolution, broadband spatial heterodyne Raman spectrometer based on field-widened grating-echelle structure.

We propose a spatial heterodyne Raman spectrometer (SHRS) based on a field-widened grating-echelle (FWGE). A normal grating is combined with an echelle grating in a conventional spatial heterodyne spectrometer to eliminate ghost images without using masks, and prevents interference among the spatial frequencies of different diffraction orders. Mathematical expressions and derivation processes are given for the spectral parameters in the FWGE-SHRS and a verification breadboard system is fabricated. The FWGE-SHRS measures Raman spectra of single chemicals and mixed targets with different integration times, laser powers, concentrations, and transparent containers. The results of the experiments demonstrate that the FWGE-SHRS is suitable for high-resolution, broadband Raman measurements for a wide range of applications.

Study on an Automatic Classification Method for Determining the Malignancy Grade of Glioma Pathological Sections Based on Hyperspectral Multi-Scale Spatial-Spectral Fusion Features.

This study describes a novel method for grading pathological sections of gliomas. Our own integrated hyperspectral imaging system was employed to characterize 270 bands of cancerous tissue samples from microarray slides of gliomas. These samples were then classified according to the guidelines developed by the World Health Organization, which define the subtypes and grades of diffuse gliomas. We explored a hyperspectral feature extraction model called SMLMER-ResNet using microscopic hyperspectral images of brain gliomas of different malignancy grades. The model combines the channel attention mechanism and multi-scale image features to automatically learn the pathological organization of gliomas and obtain hierarchical feature representations, effectively removing the interference of redundant information. It also completes multi-modal, multi-scale spatial-spectral feature extraction to improve the automatic classification of glioma subtypes. The proposed classification method demonstrated high average classification accuracy (>97.3%) and a Kappa coefficient (0.954), indicating its effectiveness in improving the automatic classification of hyperspectral gliomas. The method is readily applicable in a wide range of clinical settings, offering valuable assistance in alleviating the workload of clinical pathologists. Furthermore, the study contributes to the development of more personalized and refined treatment plans, as well as subsequent follow-up and treatment adjustment, by providing physicians with insights into the underlying pathological organization of gliomas.

Theoretical analysis of a multi-grating-based cross-dispersed spatial heterodyne spectrometer.

This paper presents a multi-grating-based cross-dispersed spatial heterodyne spectrometer (MGCDSHS). The principle of generation of two-dimensional interferograms for two cases, where the light beam is diffracted by one sub-grating or two sub-gratings, is given and equations for the interferogram parameters in these two cases are derived. An instrument design with numerical simulations is presented that demonstrates the spectrometer's ability to simultaneously record separate interferograms corresponding to different spectral features with high resolution over a broad spectral range. The design solves the mutual interference problem caused by overlapping of the interferograms, and also provides the high spectral resolution and broad spectral measurement range that cannot be achieved using conventional SHSs. Additionally, by introducing cylindrical lens groups, the MGCDSHS solves the throughput loss and light intensity reduction problems caused by direct use of multi-gratings. The MGCDSHS is compact, highly stable, and high-throughput. These advantages make the MGCDSHS suitable for high-sensitivity, high-resolution, and broadband spectral measurements.

Broadband, high-resolution spatial heterodyne Raman spectroscopy measurement based on a multi-Littrow-angle multi-grating.

This paper proposes a spatial heterodyne Raman spectrometer (SHRS) based on a multi-Littrow-angle multi-grating (MLAMG). Compared with a conventional multi-grating, the MLAMG not only provides higher spectral resolution and a broader spectral range, but is also easier to produce. A verification breadboard system is built using the MLAMG combined with four sub-gratings with a groove density of 300 gr/mm and Littrow angles of 4.6355°, 4.8536°, 5.0820°, and 5.3253°. This MLAMG-SHRS is used to obtain the Raman spectra of inorganic solids and organic solutions for different integration times, laser powers, suspension contents, and containers. The Raman spectra of mixed targets and minerals are also presented. The experiments demonstrate that the MLAMG-SHRS is suitable for broadband measurements at high spectral resolution in a wide range of potential applications.

Accurate spectrogram restoration algorithm for an echelle spectrometer based on adaptive parameters.

The echelle spectrometer is a high-resolution spectrometer that can realize transient direct readings of a full spectrum. To improve the accuracy of the spectrogram restoration model in calibration, multiple-integral time fusion, and an improved adaptive-threshold centroid algorithm are used to overcome noise and improve the accuracy of calculating the light spot position. A seven-parameter pyramid-traversal method is proposed to optimize the parameters of the spectrogram restoration model. The deviation of the spectrogram model is significantly reduced after the parameters are optimized, and the deviation curve fluctuation becomes mild, which greatly improves the model's accuracy after curve fitting.The test results show that the accuracy of the spot position determination algorithm proposed in this paper is 0.1 pixels. In addition to this, the accuracy of the spectral restoration model is controlled within 0.3 pixels in a short-wave stage and 0.7 pixels in a long-wave stage. Compared with the traditional algorithm, the accuracy of spectrogram restoration is more than two times, and the spectral calibration time is less than 45 min.

Design study of a cross-dispersed spatial heterodyne spectrometer.

A cross-dispersed spatial heterodyne spectrometer (CDSHS) that integrates a spatial heterodyne spectrometer (SHS), a reflection grating, and a cylindrical lens is presented. Expressions for the width, height, and location of the cross-dispersed interferograms corresponding to narrow spectral regions are given. An example CDSHS design, including numerical simulations of the interferogram and the spectrum, is provided to illustrate the designed system. The results show that the CDSHS can simultaneously disperse longitudinally and laterally to record interferograms corresponding to different narrow spectral regions with different rows on a charge-coupled device, and obtain independent detailed spectra simultaneously with a high signal-to-noise ratio. Additionally, high-intensity light rays at a specific wavelength in the CDSHS do not interfere with the detailed spectra of the other wavelengths. Simultaneously, the CDSHS offers advantages including high resolution, high throughput, broadband operation, compactness, and zero moving parts. The CDSHS shows great application potential in fields including multiple spectral feature measurement, weak spectral measurements.

Design study of a cross-dispersed spatial heterodyne spectrometer: erratum.

We present an erratum to our article [Opt. Express30(7), 10547 (2022)10.1364/OE.448504].

Insights into the Molecular Dynamics of Quasi-Spherical (Chloromethyl)triethylammonium Confined in a Weakly Bound Ionic Cocrystal.

Here, we report a weakly bound ionic cocrystal, (Et3NCH2Cl)2[ZnCl4], which undergoes a reversible structural phase transition owing to the switched molecular dynamics of the quasi-spherical (Et3NCH2Cl)+ cation from static to dynamic. Interestingly, a unique rolling and moving mechanism is uncovered for such a cation in the high-temperature phase, where its two methylene groups exhibit different kinetic energy barriers. This study provides a meaningful insight into the solid-state molecular dynamics of large-size quasi-spherical molecules that contain both a rigid core and flexible shell.

Research on spectral reconstruction algorithm for snapshot microlens array micro-hyperspectral imaging system.

Snapshot microlens array microscopic hyperspectral imaging systems do not require a scanning process and obtain (x,y,λ) three-dimensional data cubes in one shot. Currently, the three-dimensional spectra image data are interleaved on a charge-coupled device detector, which increases subsequent data processing difficulty. The optical design software cannot simulate actual engineering installation and adjustment results accurately and the tracking results cannot guide precise rapid online calibration of the snapshot microlens array microscopic hyperspectral imaging system. To solve these problems, we propose an accurate spectral image reconstruction model based on optical tracing, derive spatial dispersion equations for the prisms and gratings, establish an algorithm model for the correspondence between the microlens array's surface dispersion spectral distribution and its imaging position, and propose a three-dimensional spectral image reconstruction algorithm. Experimental results show that this algorithm's actual spectral calibration error is better than 0.2 nm. This meets the image processing requirements of snapshot microlens array microscopic hyperspectral systems.

Microlens array snapshot hyperspectral microscopy system for the biomedical domain.

We propose a microlens array-type snapshot hyperspectral microscope system that can provide spatial spectrum sampling according to detector frame rates for the biomedical domain. The system uses a shared optical path design. One path is used to perform direct microscopic imaging with high spatial resolution, while the other is used to collect microscopic images through a microlens array; the images are then spatially cut and reimaged such that they are spaced simultaneously by the prism-grating type hyperspectral imager's dispersion. Rapid acquisition of a three-dimensional data cube measuring 28×14×180 (x×y×λ) can be performed at the detector's frame rate. The system has a spatial resolution of 2.5 µm and can achieve 180-channel sampling of a 100 nm spectrum in the 400-800 nm spectral range with spectral resolution of approximately 0.56 nm. Spectral imaging results from biological samples show that the microlens array-type snapshot hyperspectral microscope system may potentially be applied in real-time biological spectral imaging.

Different surgical outcome and follow-up status between dMMR and pMMR colorectal cancer patients who fulfilled with Amsterdam-II criteria.

BACKGROUND: Although hereditary non-polyposis colorectal cancer (HNPCC) could be subtyped into proficient or deficient mismatch repair gene expression (pMMR or dMMR), distinct clinical features between these two subgroups patients were rarely reported. METHODS: We retrospectively analyzed 175 hereditary non-polyposis colorectal cancer (HNPCC) patients between January 1995 and December 2012. Cox proportional hazards model was used to compare the differences between two subgroups. RESULTS: Significant differences of disease free survival (DFS) and overall survival (OS) exist between dMMR and pMMR. In addition to other factors including younger mean age of diagnosis for dMMR patients (48.6 years vs. 54.3 years), operation type (more extended colectomy for dMMR 35.8% vs. 14.5%), tumor location (right colon predominance for dMMR 61.7% vs. 27.3% and more rectum cases for pMMR 41.8% vs. 11.7%), tumor differentiation (more poor differentiation for dMMR 23.3% vs. 9.0%), N staging (more N0 cases for dMMR 70.8% vs. 50.9%), more frequently presence of extra-colonic tumors for dMMR (16.7% vs.1.8%), and lower recurrence rates (9.1% vs.35.3%). Significantly different cumulative incidences of developing metachronous colorectal cancer were observed with 6.18 for pMMR patients and 20.57 person-years for dMMR patients (p < 0.001). CONCLUSIONS: Distinct clinicopathological features significantly exist between dMMR and pMMR subtypes patient, MMR status should be consider to tailor operation types and follow up surveillance between these two subgroups patients who all fulfilled with Amsterdam-II criteria.

Phylogenetic, expression and functional characterizations of the maize NLP transcription factor family reveal a role in nitrate assimilation and signaling.

Although nitrate represents an important nitrogen (N) source for maize, a major crop of dryland areas, the molecular mechanisms of nitrate uptake and assimilation remain poorly understood. Here, we identified nine maize NIN-like protein (ZmNLP) genes and analyzed the function of one member, ZmNLP3.1, in nitrate nutrition and signaling. The NLP family genes were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that most ZmNLP genes had collinear relationships to the corresponding NLPs in rice, and that the expansion of the ZmNLP family resulted from segmental duplications in the maize genome. Quantitative PCR analysis revealed the expression of ZmNLP2.1, ZmNLP2.2, ZmNLP3.1, ZmNLP3.2, ZmNLP3.3, and ZmNLP3.4 was induced by nitrate in maize roots. The function of ZmNLP3.1 was investigated by overexpressing it in the Arabidopsis nlp7-1 mutant, which is defective in the AtNLP7 gene for nitrate signaling and assimilation. Ectopic expression of ZmNLP3.1 restored the N-deficient phenotypes of nlp7-1 under nitrate-replete conditions in terms of shoot biomass, root morphology and nitrate assimilation. Furthermore, the nitrate induction of NRT2.1, NIA1, and NiR1 gene expression was recovered in the 35S::ZmNLP3.1/nlp7-1 transgenic lines, indicating that ZmNLP3.1 plays essential roles in nitrate signaling. Taken together, these results suggest that ZmNLP3.1 plays an essential role in regulating nitrate signaling and assimilation processes, and represents a valuable candidate for developing transgenic maize cultivars with high N-use efficiency.

Design and analysis of a worm gear turntable off-axis assembly method in a three-grating monochromator.

To solve the problem where the actual grating aperture decreases with an increasing scanning angle during the scanning of a three-grating monochromator, we propose an off-axis assembly method for the worm gear turntable that makes it possible to suppress this aperture reduction. We simulated and compared the traditional assembly method with the off-axis assembly method in the three-grating monochromator. Results show that the actual grating aperture can be improved by the off-axis assembly method. In fact, for any one of the three gratings, when the monochromator outputs the longest wavelength in the corresponding wavelength band, the actual grating aperture increases by 45.93%. Over the entire monochromator output band, the actual grating aperture increased by an average of 32.56% and can thus improve the monochromator's output energy. Improvement of the actual grating aperture can also reduce the stray light intensity in the monochromator and improve its output signal-to-noise ratio.

Backscattering Raman spectroscopy using multi-grating spatial heterodyne Raman spectrometer.

Spatial heterodyne Raman spectrometry (SHRS) is a spectral analysis technique used to study material structures and compositions. We propose a multi-grating SHRS system that uses a multi-grating module rather than the single grating used to terminate each arm in traditional spatial heterodyne spectrometry (SHS). The proposed system not only retains the advantages of traditional SHS but also resolves the mutual limitation between system spectral range and resolution. The increased spectral range and resolution that can be achieved in detection are dependent on the number of sub-gratings used in the module. A verification system was built using 130 gr/mm and 150 gr/mm sub-gratings and calibrated. Under different experimental conditions (including laser power, integration time, container material and thickness, pure and mixed samples, and standoff experiments), the backscattered Raman spectra of different types of targets (including organic solutions, inorganic powders, and minerals) were tested. The multi-grating SHRS shows good performance for broad spectral range and high-resolution Raman detection.

Optical design of a short-wave infrared prism-grating imaging spectrometer.

A miniaturized portable short-wave infrared imaging spectroscopy optical system is designed based on a prism-grating dispersion module. We established a prism-grating model to calculate the optimal combination of prism and grating parameters to balance spectral smile over the entire band. The design method for the telescopic system and spectroscopic system combines independent design with integrated optimization. The system's spectral smile and spectral keystone are less than 15 µm and less than half a pixel, respectively. The total optical system length is 230 mm, which meets the miniaturization requirements for airborne systems. The system's spatial resolution is 1 mrad, and its average spectral resolution is 6.2 nm. The system offers the advantages of large relative aperture, excellent imaging quality, reduced spectral smile, and spectral keystone, miniaturization, and portability.

Method for measurement of eccentricity and tilt of lenslet array integral field spectrometer.

This paper proposes a more accurate eccentricity and tilt measurement method based on Young's interference experiment. The basic principle of the method is introduced first before the method is simulated. Then the results are obtained when a to-be-adjusted focusing lens with eccentricity and tilt is simulated. The optical sensitivity also is obtained from these simulation results, and the expression for the change in optical path length caused by eccentricity and tilt is analyzed. Use of this method to detect eccentricity and tilt and assist in adjustment of the system allows the instrument to achieve higher accuracy and thus obtain improved imaging quality and spectral resolution.

Study on a wideband, variable aperture, high resolution scatterometer for planar diffraction grating stray light measurement.

Stray light is one of the important factors for evaluating the quality of gratings. Therefore, it has become an important problem in the field of grating development to measure the stray light of planar diffraction gratings accurately. For that reason, a planar grating stray light testing instrument based on a Czerny-Turner (C-T) structure has been studied. On the premise of the low stray light of the instrument itself, the instrument is capable of measuring wideband, variable aperture, and high resolution stray light for planar gratings. A scatterometer dynamic range of over nine orders has been demonstrated. Based on the scalar diffraction theory and classical Fresnel-Kirchhoff diffraction theory, the optical and mechanical model of the scatterometer is designed, which is irradiated by parallel light, and the simulation results are analyzed. The instrument realizes the measurement of the grating distribution function (GDF). And with reference to the expression form of the bidirectional reflectance distribution function (BRDF), the measurement data of the instrument is associated with the power spectral density (PSD). Through the optical integrated design and stray light suppression design, full aperture (15 mm×15 mm-200 mm×200 mm) and wideband (380-900 nm) measurement for any number of lines grating is realized, and the efficiency of equipment usage is improved. Experimental results show that based on the attenuation method, the accuracy of measurement can be 10-9 by the replacement of the neutral density filters.

High-accuracy spectral reduction algorithm for the échelle spectrometer.

A spectral reduction algorithm for an échelle spectrometer with spherical mirrors that builds a one-to-one correspondence between the wavelength and pixel position is proposed. The algorithm accuracy is improved by calculating the offset distance of the principal ray from the center of the image plane in the two-dimensional vertical direction and compensating the spectral line bending from the reflecting prism. The simulation and experimental results verify that the maximum deviation of the entire image plane is less than one pixel. This algorithm ensures that the wavelengths calculated from spectrograms have a high spectral resolution, meaning the precision from the spectral analysis reaches engineering standards of practice.

[Full-field and automatic methodology of spectral calibration for PGP imaging spectrometer].

In order to analyze spectral data quantitatively which is obtained by prism-grating-prism imaging spectrometer, spectral calibration is required in order to determine spectral characteristics of PGP imaging spectrometer, such as the center wavelength of every spectral channel, spectral resolution and spectral bending. A spectral calibration system of full field based on collimated monochromatic light method is designed. Spherical mirror is used to provide collimated light, and a freely sliding and rotating folding mirror is adopted to change the angle of incident light in order to realize full field and automatic calibration of imaging spectrometer. Experiments of spectral calibration have been done for PGP imaging spectrometer to obtain parameters of spectral performance, and accuracy analysis combined with the structural features of the entire spectral calibration system have been done. Analysis results indicate that spectral calibration accuracy of the calibration system reaches 0.1 nm, and the bandwidth accuracy reaches 1.3%. The calibration system has merits of small size, better commonality, high precision and so on, and because of adopting the control of automation, the additional errors which are caused by human are avoided. The calibration system can be used for spectral calibration of other imaging spectrometers whose structures are similar to PGP.