Jack R Grimm, Jinhui Tao, Bojana Ginovska, Arun Devaraj, Sandra D Taylor
Application of atom probe tomography to electrically non-conductive materials is typically enabled by pulsing a laser onto a sample under strong electric fields to induce field evaporation. The measured composition depends on the laser-material interaction, necessitating systematic optimization experiments. This is particularly important for hydroxyapatite (Ca10(PO4)6(OH)2), a biologically and geologically relevant mineral for which subtle compositional changes can have significant implications. Therefore, we performed a series of experiments on synthetic hydroxyapatite to systematically assess how the laser pulse energy, definition of ranges in the mass-to-charge state spectrum, and calcium charge state ratio have an impact on the measured calcium-to-phosphorous ratio and mechanism of field evaporation on separate atom probe systems equipped with ultraviolet (355 nm wavelength) and deep ultraviolet (257.5 nm) lasers. We also evaluated the stoichiometric accuracy of the simultaneous voltage pulsing mode on the deep ultraviolet system, which both reduces the background and introduces artifacts into the mass-to-charge state spectrum. Correlations between the calcium-to-phosphorus ratio and the charge state ratio and fraction of ions ranged were identified. In turn, these analyses provide guidance for improving measurement accuracy of hydroxyapatite and other insulating materials using atom probe tomography.
{"title":"Stoichiometric Measurement of Hydroxyapatite by Atom Probe Tomography: Effects of UV and Deep UV Laser-assisted Analytical Conditions.","authors":"Jack R Grimm, Jinhui Tao, Bojana Ginovska, Arun Devaraj, Sandra D Taylor","doi":"10.1093/mam/ozaf105","DOIUrl":"https://doi.org/10.1093/mam/ozaf105","url":null,"abstract":"<p><p>Application of atom probe tomography to electrically non-conductive materials is typically enabled by pulsing a laser onto a sample under strong electric fields to induce field evaporation. The measured composition depends on the laser-material interaction, necessitating systematic optimization experiments. This is particularly important for hydroxyapatite (Ca10(PO4)6(OH)2), a biologically and geologically relevant mineral for which subtle compositional changes can have significant implications. Therefore, we performed a series of experiments on synthetic hydroxyapatite to systematically assess how the laser pulse energy, definition of ranges in the mass-to-charge state spectrum, and calcium charge state ratio have an impact on the measured calcium-to-phosphorous ratio and mechanism of field evaporation on separate atom probe systems equipped with ultraviolet (355 nm wavelength) and deep ultraviolet (257.5 nm) lasers. We also evaluated the stoichiometric accuracy of the simultaneous voltage pulsing mode on the deep ultraviolet system, which both reduces the background and introduces artifacts into the mass-to-charge state spectrum. Correlations between the calcium-to-phosphorus ratio and the charge state ratio and fraction of ions ranged were identified. In turn, these analyses provide guidance for improving measurement accuracy of hydroxyapatite and other insulating materials using atom probe tomography.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 5","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145401159","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}
Abigail Carbone, Robert Sinclair, Reinhold H Dauskardt
Organic-inorganic perovskites are an emerging class of photovoltaic materials. Despite achieving power conversion efficiencies surpassing 26%, the challenge of perovskite stability including degradation during exposure to operational conditions such as light, heat, humidity, water, oxygen, and electric fields is well known. Related, perovskite instability has limited high-resolution electron imaging and characterization techniques that can be used for understanding degradation mechanisms. Here, we demonstrate perovskite device cross-section preparation using mechanical polishing in a water-free environment with cryogenic Ar ion milling. Scanning electron microscopy was then used in both backscattered electron and secondary electron imaging modes to obtain information about layer structure, grain aggregate structure, and compositional heterogeneity. Monte Carlo CASINO simulations inform optimum beam conditions and image acquisition parameters and the effects of accelerating voltage, dwell times, and frame averaging for practical image acquisition are reported.
{"title":"Advancing Cross-Sectional Scanning Electron Microscopy of Perovskite Solar Cells.","authors":"Abigail Carbone, Robert Sinclair, Reinhold H Dauskardt","doi":"10.1093/mam/ozaf067","DOIUrl":"https://doi.org/10.1093/mam/ozaf067","url":null,"abstract":"<p><p>Organic-inorganic perovskites are an emerging class of photovoltaic materials. Despite achieving power conversion efficiencies surpassing 26%, the challenge of perovskite stability including degradation during exposure to operational conditions such as light, heat, humidity, water, oxygen, and electric fields is well known. Related, perovskite instability has limited high-resolution electron imaging and characterization techniques that can be used for understanding degradation mechanisms. Here, we demonstrate perovskite device cross-section preparation using mechanical polishing in a water-free environment with cryogenic Ar ion milling. Scanning electron microscopy was then used in both backscattered electron and secondary electron imaging modes to obtain information about layer structure, grain aggregate structure, and compositional heterogeneity. Monte Carlo CASINO simulations inform optimum beam conditions and image acquisition parameters and the effects of accelerating voltage, dwell times, and frame averaging for practical image acquisition are reported.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690926","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}
Histological staining is essential for understanding bone structure and pathology; however, variations in decalcification agents can compromise reproducibility. We have previously developed a novel osteochondral staining method, Join of the Five dyes Revealing coLlagenous tissue (JFRL) staining, that is independent of the decalcification method. To promote its widespread adoption, this study confirms the robustness of JFRL staining through intra- and inter-laboratory validation. JFRL staining demonstrated consistent patterns across different manufacturers and facilities, with proper dehydration steps being crucial for optimal results. We applied JFRL staining to diverse vertebrate species prepared under various fixation and decalcification conditions to effectively visualize species-specific bone structures, including distinct osteoid and mineralized bone features from fish to large mammals. Furthermore, JFRL staining proved useful in evaluating bone biomaterials within defect models and clearly depicts the complex architecture of bone-healing processes and material integration. The staining qualitatively distinguished osteoid, mineralized bone, hyaline cartilage, and bone cells of different colors across all applications. These findings establish JFRL staining as a robust and versatile method for bone histology. Future studies focusing on quantitative assessment and pathological applications will prove that JFRL staining presents a reliable tool for both basic research and clinical diagnostics of bone disorders.
{"title":"Multi-laboratory Validation of Join of the Five Dyes Revealing Collagenous Tissue (JFRL) Staining for Bone Histology Across Animal Species and Bone Implant Materials.","authors":"Erika Tsuji, Kanako Sumi, Natsuko Tsuzuki, Daisuke Kondoh, Masashi Tsujio, Marina Hosotani, Takashi Namba, Shoichi Wakitani, Osamu Ichii, Ko Nakanishi, Teppei Nakamura","doi":"10.1093/mam/ozaf058","DOIUrl":"https://doi.org/10.1093/mam/ozaf058","url":null,"abstract":"<p><p>Histological staining is essential for understanding bone structure and pathology; however, variations in decalcification agents can compromise reproducibility. We have previously developed a novel osteochondral staining method, Join of the Five dyes Revealing coLlagenous tissue (JFRL) staining, that is independent of the decalcification method. To promote its widespread adoption, this study confirms the robustness of JFRL staining through intra- and inter-laboratory validation. JFRL staining demonstrated consistent patterns across different manufacturers and facilities, with proper dehydration steps being crucial for optimal results. We applied JFRL staining to diverse vertebrate species prepared under various fixation and decalcification conditions to effectively visualize species-specific bone structures, including distinct osteoid and mineralized bone features from fish to large mammals. Furthermore, JFRL staining proved useful in evaluating bone biomaterials within defect models and clearly depicts the complex architecture of bone-healing processes and material integration. The staining qualitatively distinguished osteoid, mineralized bone, hyaline cartilage, and bone cells of different colors across all applications. These findings establish JFRL staining as a robust and versatile method for bone histology. Future studies focusing on quantitative assessment and pathological applications will prove that JFRL staining presents a reliable tool for both basic research and clinical diagnostics of bone disorders.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637613","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}
Kyvia L C Costa, Fernanda C R Dias, Fabiana C S A Melo, Marcos L M Gomes, Sérgio L P Matta
Lead is a widespread environmental pollutant that affects biological systems, particularly the male reproductive system. This study evaluated the effects of subchronic lead exposure on the testicular parenchyma of adult Wistar rats. Animals were divided into five groups: one control and four treated with increasing doses of lead acetate (16, 32, 64, and 128 mg/kg/day). Testicular tissues were analyzed using light and transmission electron microscopy, along with measurements of testicular lead concentration and antioxidant enzyme activity (SOD and CAT). Histopathological alterations included vacuolization, germ cell desquamation, apoptotic bodies, lipid droplets, and blood-testis barrier rupture. A dose-dependent reduction in seminiferous epithelium height and germ cell population was observed, along with an enlarged tubular lumen. These structural changes resulted in decreased sperm production and sperm reserves, particularly at higher lead doses. Additionally, lead exposure significantly reduced the activity of SOD and CAT enzymes, indicating oxidative stress. In conclusion, subchronic lead exposure disrupts testicular structure and function by inducing oxidative damage, leading to impaired spermatogenesis and fertility.
{"title":"Deleterious Effects of Lead Acetate Intake on the Spermatogenic Process in Adult Wistar Rats.","authors":"Kyvia L C Costa, Fernanda C R Dias, Fabiana C S A Melo, Marcos L M Gomes, Sérgio L P Matta","doi":"10.1093/mam/ozaf074","DOIUrl":"10.1093/mam/ozaf074","url":null,"abstract":"<p><p>Lead is a widespread environmental pollutant that affects biological systems, particularly the male reproductive system. This study evaluated the effects of subchronic lead exposure on the testicular parenchyma of adult Wistar rats. Animals were divided into five groups: one control and four treated with increasing doses of lead acetate (16, 32, 64, and 128 mg/kg/day). Testicular tissues were analyzed using light and transmission electron microscopy, along with measurements of testicular lead concentration and antioxidant enzyme activity (SOD and CAT). Histopathological alterations included vacuolization, germ cell desquamation, apoptotic bodies, lipid droplets, and blood-testis barrier rupture. A dose-dependent reduction in seminiferous epithelium height and germ cell population was observed, along with an enlarged tubular lumen. These structural changes resulted in decreased sperm production and sperm reserves, particularly at higher lead doses. Additionally, lead exposure significantly reduced the activity of SOD and CAT enzymes, indicating oxidative stress. In conclusion, subchronic lead exposure disrupts testicular structure and function by inducing oxidative damage, leading to impaired spermatogenesis and fertility.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883188","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}
Aurélie Dehlinger, Valentina Alberini, Vladimir Usatikov, Céline Dyhring, Sarah Jung, Jonas Grage, Daniel Grötzsch, Johannes Tümmler, Stefan Rehbein, Holger Stiel, Birgit Kanngießer, Christian Seim
Method development for laboratory-based X-ray microscopes operating in the water-window range invariably involves the development of the X-ray source as well. This paper presents major upgrades to the laboratory soft X-ray microscope (L-TXM) plasma chamber and data analysis protocol. Characterization of the laser-plasma source demonstrates improved performance, while a proof-of-principle tomogram of a diatom showcases a robust data treatment protocol and the system's capabilities for three-dimensional imaging and segmentation. These developments mark significant progress toward making L-TXM a more robust and user-friendly tool for soft X-ray microscopy applications.
{"title":"Laboratory-Based Soft X-Ray Tomography: A Novel Laser Design, Source Monitoring, and Data-Processing Workflow.","authors":"Aurélie Dehlinger, Valentina Alberini, Vladimir Usatikov, Céline Dyhring, Sarah Jung, Jonas Grage, Daniel Grötzsch, Johannes Tümmler, Stefan Rehbein, Holger Stiel, Birgit Kanngießer, Christian Seim","doi":"10.1093/mam/ozaf073","DOIUrl":"10.1093/mam/ozaf073","url":null,"abstract":"<p><p>Method development for laboratory-based X-ray microscopes operating in the water-window range invariably involves the development of the X-ray source as well. This paper presents major upgrades to the laboratory soft X-ray microscope (L-TXM) plasma chamber and data analysis protocol. Characterization of the laser-plasma source demonstrates improved performance, while a proof-of-principle tomogram of a diatom showcases a robust data treatment protocol and the system's capabilities for three-dimensional imaging and segmentation. These developments mark significant progress toward making L-TXM a more robust and user-friendly tool for soft X-ray microscopy applications.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883192","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}
William Mottay, Jeremy Landes, Alain Portavoce, Benjamin Klaes, Frederic Danoix, Philippe Maugis, Pierre Stocker, Carine Perrin-Pellegrino, Khalid Hoummada
Atom probe tomography (APT) is now routinely used to study solute atom segregation at crystalline defects in different materials. The present study reports unexpected observations concerning carbon (C) segregation at dislocations in APT volumes analyzed from two different industrial steel grades. APT analyses reveal that C segregation at dislocations could only be observed with Mo co-segregation. Indeed, transmission electron microscopy (TEM) observations on APT tips and correlative TEM-APT analysis show that despite dislocations being present in the samples prior to APT analyses, C segregation was not observed in the absence of Mo segregation. Statistics on the distribution of C composition in the different APT volumes from Mo-free steels show important discrepancies, with 35% of the volumes exhibiting C content in solid solution five times higher than expected. It is concluded that APT measurements of both C segregation at dislocations and C content in solution in iron may be incorrect due to the possibility of dislocations leaving the APT samples when subjected to a high electric field before or during field evaporation.
{"title":"Startling C Behavior in Mo-Free Steel Atom Probe Tomography Volumes.","authors":"William Mottay, Jeremy Landes, Alain Portavoce, Benjamin Klaes, Frederic Danoix, Philippe Maugis, Pierre Stocker, Carine Perrin-Pellegrino, Khalid Hoummada","doi":"10.1093/mam/ozaf078","DOIUrl":"https://doi.org/10.1093/mam/ozaf078","url":null,"abstract":"<p><p>Atom probe tomography (APT) is now routinely used to study solute atom segregation at crystalline defects in different materials. The present study reports unexpected observations concerning carbon (C) segregation at dislocations in APT volumes analyzed from two different industrial steel grades. APT analyses reveal that C segregation at dislocations could only be observed with Mo co-segregation. Indeed, transmission electron microscopy (TEM) observations on APT tips and correlative TEM-APT analysis show that despite dislocations being present in the samples prior to APT analyses, C segregation was not observed in the absence of Mo segregation. Statistics on the distribution of C composition in the different APT volumes from Mo-free steels show important discrepancies, with 35% of the volumes exhibiting C content in solid solution five times higher than expected. It is concluded that APT measurements of both C segregation at dislocations and C content in solution in iron may be incorrect due to the possibility of dislocations leaving the APT samples when subjected to a high electric field before or during field evaporation.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961063","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}
Tianbi Zhang, Ruth M Birch, Graeme J Francolini, Ebru Karakurt Uluscu, Ben Britton
Compact direct electron detectors are becoming increasingly popular in electron microscopy applications including electron backscatter diffraction, as they offer an opportunity for low cost and accessible microstructural analysis. In this work, we explore how one of these commercial devices based on the Timepix chip can be optimized to obtain high-quality data quickly and easily, through careful systematic analysis of a variety of samples, including: semiconductor silicon, commercially pure nickel, a dual phase titanium-molybdenum alloy, and a silicon carbide ceramic matrix composite. Our findings provide strategies for very fast collection of orientation maps, including at low voltage (5-10 keV) and low beam current conditions. Additionally, strategies for collection of very high-quality EBSD patterns are demonstrated that have significant potential for advanced EBSD applications (e.g., elastic strain mapping).
{"title":"Practical Considerations for Crystallographic and Microstructure Mapping With Direct Electron Detector-Based Electron Backscatter Diffraction.","authors":"Tianbi Zhang, Ruth M Birch, Graeme J Francolini, Ebru Karakurt Uluscu, Ben Britton","doi":"10.1093/mam/ozaf076","DOIUrl":"https://doi.org/10.1093/mam/ozaf076","url":null,"abstract":"<p><p>Compact direct electron detectors are becoming increasingly popular in electron microscopy applications including electron backscatter diffraction, as they offer an opportunity for low cost and accessible microstructural analysis. In this work, we explore how one of these commercial devices based on the Timepix chip can be optimized to obtain high-quality data quickly and easily, through careful systematic analysis of a variety of samples, including: semiconductor silicon, commercially pure nickel, a dual phase titanium-molybdenum alloy, and a silicon carbide ceramic matrix composite. Our findings provide strategies for very fast collection of orientation maps, including at low voltage (5-10 keV) and low beam current conditions. Additionally, strategies for collection of very high-quality EBSD patterns are demonstrated that have significant potential for advanced EBSD applications (e.g., elastic strain mapping).</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961085","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}
Chia-Hao Lee, Steven E Zeltmann, Dasol Yoon, Desheng Ma, David A Muller
Electron ptychography has recently achieved unprecedented resolution, offering valuable insights across diverse material systems, including in three dimensions. However, high-quality ptychographic reconstruction is computationally expensive and time consuming, requiring a significant amount of manually tuning even for experts. Additionally, essential tools for ptychographic analysis are often scattered across multiple software packages, with some advanced features available only in costly commercial software like MATLAB. To address these challenges, we introduce PtyRAD (Ptychographic Reconstruction with Automatic Differentiation), an open-source software framework offers a comprehensive, flexible, and computationally efficient solution for electron ptychography. PtyRAD provides seamless optimization of multiple parameters-such as sample thickness, local tilts, probe positions, and mixed probe and object modes-using gradient-based methods with automatic differentiation. By utilizing PyTorch's highly optimized tensor operations, PtyRAD achieves up to a 24× speedup in reconstruction time compared to existing packages without compromising image quality. In addition, we propose a real-space depth regularization, which avoids wrap-around artifacts and can be useful for twisted two-dimensional material datasets and vertical heterostructures. Moreover, PtyRAD integrates a Bayesian optimization workflow that streamlines hyperparameter selection. We hope the open-source nature of PtyRAD will foster reproducibility and community-driven development for future advances in ptychographic imaging.
电子印刷术最近取得了前所未有的分辨率,提供了跨不同材料系统的有价值的见解,包括三维。然而,高质量的型图重建在计算上昂贵且耗时,即使是专家也需要大量的手动调整。此外,用于型图分析的基本工具通常分散在多个软件包中,其中一些高级功能仅在昂贵的商业软件(如MATLAB)中可用。为了应对这些挑战,我们引入了PtyRAD (Ptychographic Reconstruction with Automatic Differentiation),这是一个开源软件框架,为电子平面摄影提供了一个全面、灵活和计算效率高的解决方案。PtyRAD提供了多个参数的无缝优化-如样品厚度,局部倾斜,探头位置,以及混合探头和对象模式-使用梯度为基础的方法与自动区分。通过利用PyTorch高度优化的张量操作,与现有软件包相比,PtyRAD在不影响图像质量的情况下实现了高达24倍的重建时间加速。此外,我们提出了一种真实空间深度正则化,它避免了缠绕伪影,可以用于扭曲的二维材料数据集和垂直异质结构。此外,PtyRAD集成了一个贝叶斯优化工作流,简化了超参数选择。我们希望PtyRAD的开源性质将促进可重复性和社区驱动的发展,为未来的病理成像进步。
{"title":"PtyRAD: A High-Performance and Flexible Ptychographic Reconstruction Framework with Automatic Differentiation.","authors":"Chia-Hao Lee, Steven E Zeltmann, Dasol Yoon, Desheng Ma, David A Muller","doi":"10.1093/mam/ozaf070","DOIUrl":"10.1093/mam/ozaf070","url":null,"abstract":"<p><p>Electron ptychography has recently achieved unprecedented resolution, offering valuable insights across diverse material systems, including in three dimensions. However, high-quality ptychographic reconstruction is computationally expensive and time consuming, requiring a significant amount of manually tuning even for experts. Additionally, essential tools for ptychographic analysis are often scattered across multiple software packages, with some advanced features available only in costly commercial software like MATLAB. To address these challenges, we introduce PtyRAD (Ptychographic Reconstruction with Automatic Differentiation), an open-source software framework offers a comprehensive, flexible, and computationally efficient solution for electron ptychography. PtyRAD provides seamless optimization of multiple parameters-such as sample thickness, local tilts, probe positions, and mixed probe and object modes-using gradient-based methods with automatic differentiation. By utilizing PyTorch's highly optimized tensor operations, PtyRAD achieves up to a 24× speedup in reconstruction time compared to existing packages without compromising image quality. In addition, we propose a real-space depth regularization, which avoids wrap-around artifacts and can be useful for twisted two-dimensional material datasets and vertical heterostructures. Moreover, PtyRAD integrates a Bayesian optimization workflow that streamlines hyperparameter selection. We hope the open-source nature of PtyRAD will foster reproducibility and community-driven development for future advances in ptychographic imaging.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883196","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}
A DigitalMicrograph® script RAPID-DM (RAtio method Pattern InDexing) has been developed, which allows instant on-site indexing of zone axis electron diffraction patterns of cubic lattices using the Rn ratio principle. In addition to indexing spot electron diffraction patterns, the program is also capable of indexing Kikuchi patterns taken from or near a zone axis. Both cases are demonstrated by examples for silicon. The program has a guided workflow and requires only three user-defined lines or Kikuchi bands for indexing. RAPID-DM has been extensively tested and verified to work reliably with both calibrated and noncalibrated zone axis patterns and allows the user to easily evaluate whether the material under examination is cubic, pseudo-cubic, or neither. For calibrated patterns, the program provides an average value of the cubic lattice parameter, which can serve for phase identification in connection with a structural database or it can simply be used to verify the material under investigation. In its current state, the developed script has proved to be a valuable add-on to the DigitalMicrograph® platform in the authors' service laboratory, as it greatly simplifies on-site crystallographic analysis of electron diffraction patterns of steels, alloys, and ceramics, which frequently form cubic or pseudo-cubic structures.
{"title":"RAPID-DM: A DigitalMicrograph® Script for On-Site Indexing of Zone Axis Aligned Electron Diffraction Patterns of Cubic Lattices.","authors":"Vasilis A Maroufidis, Thomas E Weirich","doi":"10.1093/mam/ozaf060","DOIUrl":"10.1093/mam/ozaf060","url":null,"abstract":"<p><p>A DigitalMicrograph® script RAPID-DM (RAtio method Pattern InDexing) has been developed, which allows instant on-site indexing of zone axis electron diffraction patterns of cubic lattices using the Rn ratio principle. In addition to indexing spot electron diffraction patterns, the program is also capable of indexing Kikuchi patterns taken from or near a zone axis. Both cases are demonstrated by examples for silicon. The program has a guided workflow and requires only three user-defined lines or Kikuchi bands for indexing. RAPID-DM has been extensively tested and verified to work reliably with both calibrated and noncalibrated zone axis patterns and allows the user to easily evaluate whether the material under examination is cubic, pseudo-cubic, or neither. For calibrated patterns, the program provides an average value of the cubic lattice parameter, which can serve for phase identification in connection with a structural database or it can simply be used to verify the material under investigation. In its current state, the developed script has proved to be a valuable add-on to the DigitalMicrograph® platform in the authors' service laboratory, as it greatly simplifies on-site crystallographic analysis of electron diffraction patterns of steels, alloys, and ceramics, which frequently form cubic or pseudo-cubic structures.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883197","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}
Sean H Mills, Christoph Gammer, Alex Lin, Aaron Kohnert, Claire Chisholm, Khalid Hattar, Peter Ercius, Peter Hosemann, Andrew M Minor
Irradiation produces a distribution of defect sizes in materials, with the smallest defects often below one nanometer in size and approaching the scale of a single unit cell in metals. While high-resolution scanning transmission electron microscopy (STEM)-based imaging can directly image structures at this level, techniques such as four-dimensional STEM (4D-STEM) enable characterization of materials across large fields of view, capturing a more representative volume that can be valuable for quantifying defects, their distributions, and the associated strain fields. Here we present a combined HRSTEM and 4D-STEM approach to study the model system of He bubble implantation in an Au thin film. The present work is of general interest for the study of materials in extreme environments, as it demonstrates an effective way to characterize even the tiniest sub-nanometer sized He bubbles in addition to larger irradiation defects.
{"title":"Tiny Bubbles: Combined HR(S)TEM and 4D-STEM Analysis of Sub-Nanometer He Bubbles in Au.","authors":"Sean H Mills, Christoph Gammer, Alex Lin, Aaron Kohnert, Claire Chisholm, Khalid Hattar, Peter Ercius, Peter Hosemann, Andrew M Minor","doi":"10.1093/mam/ozaf072","DOIUrl":"10.1093/mam/ozaf072","url":null,"abstract":"<p><p>Irradiation produces a distribution of defect sizes in materials, with the smallest defects often below one nanometer in size and approaching the scale of a single unit cell in metals. While high-resolution scanning transmission electron microscopy (STEM)-based imaging can directly image structures at this level, techniques such as four-dimensional STEM (4D-STEM) enable characterization of materials across large fields of view, capturing a more representative volume that can be valuable for quantifying defects, their distributions, and the associated strain fields. Here we present a combined HRSTEM and 4D-STEM approach to study the model system of He bubble implantation in an Au thin film. The present work is of general interest for the study of materials in extreme environments, as it demonstrates an effective way to characterize even the tiniest sub-nanometer sized He bubbles in addition to larger irradiation defects.</p>","PeriodicalId":18625,"journal":{"name":"Microscopy and Microanalysis","volume":"31 4","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883198","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}