Microscopy and Microanalysis最新文献_第4页

Bridging Histopathology and Radiomics Toward Prognosis of Metastasis in Early Breast Cancer. 架起组织病理学与放射组学的桥梁，预测早期乳腺癌的转移。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-21 DOI: 10.1093/mam/ozae057

Marko Radulović, Xingyu Li, Goran J Djuričić, Jelena Milovanović, Nataša Todorović Raković, Tijana Vujasinović, Dušan Banovac, Ksenija Kanjer

{"title":"Bridging Histopathology and Radiomics Toward Prognosis of Metastasis in Early Breast Cancer.","authors":"Marko Radulović, Xingyu Li, Goran J Djuričić, Jelena Milovanović, Nataša Todorović Raković, Tijana Vujasinović, Dušan Banovac, Ksenija Kanjer","doi":"10.1093/mam/ozae057","DOIUrl":"10.1093/mam/ozae057","url":null,"abstract":"Tumor histomorphology is crucial for the prognostication of breast cancer outcomes because it contains histological, cellular, and molecular tumor heterogeneity related to metastatic potential. To enhance breast cancer prognosis, we aimed to apply radiomics analysis-traditionally used in 3D scans-to 2D histopathology slides. This study tested radiomics analysis in a cohort of 92 breast tumor specimens for outcome prognosis, addressing -omics dimensionality by comparing models with moderate and high feature counts, using least absolute shrinkage and selection operator for feature selection and machine learning for prognostic modeling. In the test folds, models with radiomics features [area under the curves (AUCs) range 0.799-0.823] significantly outperformed the benchmark model, which only included clinicopathological (CP) parameters (AUC = 0.584). The moderate-dimensionality model with 11 CP + 93 radiomics features matched the performance of the highly dimensional models with 1,208 radiomics or 11 CP + 1,208 radiomics features, showing average AUCs of 0.823, 0.799, and 0.807 and accuracies of 79.8, 79.3, and 76.6%, respectively. In conclusion, our application of deep texture radiomics analysis to 2D histopathology showed strong prognostic performance with a moderate-dimensionality model, surpassing a benchmark based on standard CP parameters, indicating that this deep texture histomics approach could potentially become a valuable prognostic tool.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Application of the EBSD Technique in the Study of Porosity and Permeability in Deformation Bands in Sandstone. 应用 EBSD 技术研究砂岩变形带的孔隙度和渗透性。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-21 DOI: 10.1093/mam/ozae070

Flávia Priscila Souza Afonso, Leonardo Lagoeiro, Haakon Fossen, Paola Ferreira Barbosa, Celeste Bertassoni Pinto, Camila Gomes Peçanha de Souza

{"title":"Application of the EBSD Technique in the Study of Porosity and Permeability in Deformation Bands in Sandstone.","authors":"Flávia Priscila Souza Afonso, Leonardo Lagoeiro, Haakon Fossen, Paola Ferreira Barbosa, Celeste Bertassoni Pinto, Camila Gomes Peçanha de Souza","doi":"10.1093/mam/ozae070","DOIUrl":"10.1093/mam/ozae070","url":null,"abstract":"Deformation bands are common constituents of porous clastic fluid reservoirs. Various techniques have been used to study deformation band structure and the associated changes in porosity and permeability. However, the use of electron backscatter diffraction technique is limited. Thus, more information is needed regarding the crystallographic relationships between detrital crystals, which can significantly impact reservoir rock quality. We employ microscopic and microstructural investigation techniques to analyze the influence of cataclastic deformation bands on pore space. Porosity measurements of the Cretaceous Ilhas Group sandstone in NE Brazil, obtained through computerized microtomography, indicate that the undeformed domains exhibit a total porosity of up to 13%. In contrast, this porosity is slightly over 1% in the deformation bands. Scanning electron microscopy analyses revealed the presence of grain fragmentation and dissolution microstructures, along with cement-filling pre-existing pores. The electron backscatter diffraction analyses indicated extensive grain fragmentation and minimal contribution from intracrystalline plasticity as a deformation mechanism. However, the c axes of quartz crystals roughly align parallel to the orientation of the deformation band. In summary, we have confirmed and quantified the internal changes in a deformation band cluster, with grain size reduction and associated compaction as the main mechanism supported by quartz cementation.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Employing Constrained Nonnegative Matrix Factorization for Microstructure Segmentation. 利用受限非负矩阵因式分解进行微结构分割

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-21 DOI: 10.1093/mam/ozae056

Ashish Chauniyal, Pascal Thome, Markus Stricker

引用次数: 0

Probing Defectivity Beneath the Hydrocarbon Blanket in 2D hBN Using TEM-EELS. 利用 TEM-EELS 勘探二维 hBN 碳氢化合物薄层下的缺陷。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-21 DOI: 10.1093/mam/ozae064

Dana O Byrne, Jim Ciston, Frances I Allen

{"title":"Probing Defectivity Beneath the Hydrocarbon Blanket in 2D hBN Using TEM-EELS.","authors":"Dana O Byrne, Jim Ciston, Frances I Allen","doi":"10.1093/mam/ozae064","DOIUrl":"10.1093/mam/ozae064","url":null,"abstract":"The controlled creation and manipulation of defects in 2D materials has become increasingly popular as a means to design and tune new material functionalities. However, defect characterization by direct atomic-scale imaging is often severely limited by surface contamination due to a blanket of hydrocarbons. Thus, analysis techniques that can characterize atomic-scale defects despite the contamination layer are advantageous. In this work, we take inspiration from X-ray absorption spectroscopy and use broad-beam electron energy loss spectroscopy (EELS) to characterize defect structures in 2D hexagonal boron nitride (hBN) based on averaged fine structure in the boron K-edge. Since EELS is performed in a transmission electron microscope (TEM), imaging can be performed in-situ to assess contamination levels and other factors such as tears in the fragile 2D sheets, which can affect the spectroscopic analysis. We demonstrate the TEM-EELS technique for 2D hBN samples irradiated with different ion types and doses, finding spectral signatures indicative of boron-oxygen bonding that can be used as a measure of sample defectiveness depending on the ion beam treatment. We propose that even in cases where surface contamination has been mitigated, the averaging-based TEM-EELS technique can be useful for efficient sample surveys to support atomically resolved EELS experiments.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identifying Sample Provenance From SEM/EDS Automated Particle Analysis via Few-Shot Learning Coupled With Similarity Graph Clustering. 通过少镜头学习与相似性图聚类从 SEM/EDS 自动粒子分析中识别样品来源。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-21 DOI: 10.1093/mam/ozae068

Jasmine Eshun, Natalie C Lamar, Sinan G Aksoy, Sarah Akers, Benjamin Garcia, Heather Cunningham, George Chin, Jenna A Bilbrey

{"title":"Identifying Sample Provenance From SEM/EDS Automated Particle Analysis via Few-Shot Learning Coupled With Similarity Graph Clustering.","authors":"Jasmine Eshun, Natalie C Lamar, Sinan G Aksoy, Sarah Akers, Benjamin Garcia, Heather Cunningham, George Chin, Jenna A Bilbrey","doi":"10.1093/mam/ozae068","DOIUrl":"10.1093/mam/ozae068","url":null,"abstract":"Automated particle analysis (APA) provides a vast amount of compositional data via energy-dispersive X-ray spectroscopy along with size and shape data via scanning electron microscopy for individual particles in a sample. In many instances, APA data are leveraged to support identification of the source of a sample based on the detection of particles of a specific composition. Often, the particles that provide context make up a minuscule portion of the sample. Additionally, the interpretation of complex samples can be difficult due to the diversity of compositions both in the mixture and within a particle. In this work, we demonstrate a method to compute and cluster similarity graphs that describe inter-particle relationships within a sample using a multi-modal few-shot learning neural network. As a proof-of-concept, we show that samples known to have been exposed to gunshot residue can be distinguished from samples occasionally mistaken for gunshot residue. Our workflow builds upon standard APA techniques and data processing methods to unveil additional information in a readily interpretable and quantitatively comparable format.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Wave Optical Modeling of the SEM Column From Source to Specimen. 扫描电镜柱从光源到试样的波光学建模。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-19 DOI: 10.1093/mam/ozae072

Surya Kamal, Yongjian Zhou, Zizhou Gong

{"title":"Wave Optical Modeling of the SEM Column From Source to Specimen.","authors":"Surya Kamal, Yongjian Zhou, Zizhou Gong","doi":"10.1093/mam/ozae072","DOIUrl":"https://doi.org/10.1093/mam/ozae072","url":null,"abstract":"Probe formation in scanning electron microscope (SEM) is often reduced to objective lens action modeling based on a point-spread function or Fourier transforms. In this study, we present the first complete wave optical modeling of the whole SEM column based on plane-by-plane propagation of the electron beam wavefunction without simplifying the optical system. We identify the challenges in plane-by-plane beam propagation and show how sampling limitations produce aliased results. Through a careful selection and combination of propagators, we have developed a general wave optical propagation method that is able to overcome the aliasing problem to achieve the appropriate probe widths. Using a two-step propagator, we show that it is possible to model the electron beam distribution throughout the column from the virtual source plane to the specimen plane. We also show that our results from the wave optical simulations are consistent with the geometrical theory of probe formation. Finally, as a direct application of this method, we demonstrated that the combined effect of aberrations in the condenser lens and the probe forming objective lens cannot be accurately represented using only the objective lens. Designing beam shaping experiments and studying the effect of partial coherence can be some novel applications.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ecofaunistic Study and Egg Morphology: Egg Laying Behavior of Hydrometra stagnorum (Linnaeus, 1753) (Gerromorpha: Heteroptera) Newly Recorded From the Karabük Province of Western Black Sea (Türkiye). 生态群落研究与卵形态学：西黑海卡拉比克省（土耳其）新记录的水螅（Hydrometra stagnorum）（林尼厄斯，1753 年）（啮齿目：异翅目）产卵行为。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-12 DOI: 10.1093/mam/ozae073

Hakan Ozdamar, Suat Kiyak

引用次数: 0

A Concept of Local Coordination Number for the Characterization of Solute Clusters within Atom Probe Tomography Data. 用于描述原子探针断层成像数据中溶质团簇特征的局部配位数概念。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-08-07 DOI: 10.1093/mam/ozae074

Mykola Lazarev, John Banhart

{"title":"A Concept of Local Coordination Number for the Characterization of Solute Clusters within Atom Probe Tomography Data.","authors":"Mykola Lazarev, John Banhart","doi":"10.1093/mam/ozae074","DOIUrl":"https://doi.org/10.1093/mam/ozae074","url":null,"abstract":"Identifying clusters of solute atoms in a matrix of solvent atoms helps to understand precipitation phenomena in alloys, for example, during the age hardening of certain aluminum alloys. Atom probe tomography datasets can deliver such information, provided that appropriate cluster identification routines are available. We investigate algorithms based on the local composition of the neighborhood of solute atoms and compare them with traditional approaches based on the local solute number density, such as the maximum separation distance method. For an ideal solid solution, the pair correlation functions of the kth nearest solute atom in the coordination number representation are derived, and the percolation threshold and the size distribution of clusters are studied. A criterion for selecting optimal control parameters based on maximizing the phase separation by the degree of clustering is proposed for a two-phase system. A map of phase compositions accessible for cluster analysis is constructed. The coordination number approach reduces the influence of density variations commonly observed in atom probe tomography data. Finally, a practical cluster analysis technique applied to the early stages of aluminum alloy aging is described.","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Revisiting Compositional Accuracy of Carbides Using a Decreased Detector Efficiency in a LEAP 6000 XR Atom Probe Instrument. 利用 LEAP 6000 XR 原子探针仪器中降低的探测器效率重新审视碳化物的成分准确性。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-07-31 DOI: 10.1093/mam/ozae069

Severin Jakob, Mattias Thuvander

引用次数: 0

Analysis of Water Ice in Nanoporous Copper Needles Using Cryo Atom Probe Tomography. 利用低温原子探针断层扫描分析纳米多孔铜针中的水冰。

IF 2.9 4区工程技术

Microscopy and Microanalysis Pub Date : 2024-07-19 DOI: 10.1093/mam/ozae062

Levi Tegg, Ingrid E McCarroll, Se-Ho Kim, Renelle Dubosq, Eric V Woods, Ayman A El-Zoka, Baptiste Gault, Julie M Cairney

引用次数: 0