Article updates

00_introduction.md

@@ -3,26 +3,26 @@ title: Introduction
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 Sample preparation for scanning/transmission electron microscopy (S/TEM) is a critical and challenging aspect of materials characterization.
-Conventional methods for producing the ultra-thin, <100 nm,samples typically required for S/TEM analysis [@https://doi.org/10.1007/978-1-4419-9244-4_5; @https://doi.org/10.1007/978-0-387-76501-3_10] are labor-intensive, often requiring hours to days of work by highly trained specialists.
+Conventional methods for producing the ultra-thin, <100 nm samples typically required for S/TEM analysis [@https://doi.org/10.1007/978-1-4419-9244-4_5; @https://doi.org/10.1007/978-0-387-76501-3_10] are labor-intensive, often requiring hours to days of work by highly trained specialists.
 The ultra-thin sections must be representative of the bulk material while minimizing preparation-induced artifacts, such as contamination, and chemical and structural alteration.
 Sample thickness must be carefully controlled to suit both the sample heterogeneity and the types of analyses planned.
-Excessive thickness obscures sample features,  compromises both high-resolution image contrast and  electron energy loss spectrum quality.
+Excessive thickness obscures sample features, compromises both high-resolution image contrast and electron energy loss spectrum quality.
 Likewise, insufficient thickness compromises structural integrity and may result in the loss of critical microstructural information, as well as reduced image and spectral intensity.
 These challenges are compounded by the diverse range of materials studied and the growing demand for site-specific analyses.
 
 Continuous refinement of TEM sample preparation methods over more than 7 decades has greatly expanded the range of materials that can be analyzed effectively at ever more demanding requirements for spatial resolution and spectroscopic sensitivity. 
 Electrolytic etching, mechanical polishing, broad-beam ion milling, mechanical grinding and drop casting, all have useful application histories [@blackham1993applications; @https://doi.org/10.1006/anbo.2001.1367; @https://doi.org/10.1007/978-1-4419-9244-4_5].
 In recent years, the two most popular sample preparation methods are ultramicrotomy, particularly for soft materials, but also for mineralogical samples and fine-grained composites, and focused ion beam (FIB) milling for thin films and bulk materials, and anything site-specific. 
-In FIB milling cross-section preparation, a  rastered beam of  Ga+, or more recently a noble gas plasma, mills out a membrane of the target material. 
+In FIB milling cross-section preparation, a rastered beam of Ga+, or more recently a noble gas plasma, mills out a membrane of the target material. 
 FIB preparation is now the default for most TEM studies of hard materials, due to the relative ease with which one can prepare uniform thickness, site-specific cross-sections of multiphase-materials.
 However, FIB instruments are an order of magnitude more expensive than microtomes, and significantly more wasteful of sample volume when preparing serial sections.  
-In ultramicrotomy sectioning,  a sharp blade shaves a series of serial slices from a mounted sample. This method was first developed in the 1950s [@https://doi.org/10.3181/00379727-74-17931; @https://doi.org/10.1002/ar.1091170403; @https://doi.org/10.1002/jcp.1030420103] for sectioning biological specimens.   
+In ultramicrotomy sectioning, a sharp blade shaves a series of serial slices from a mounted sample. This method was first developed in the 1950s [@https://doi.org/10.3181/00379727-74-17931; @https://doi.org/10.1002/ar.1091170403; @https://doi.org/10.1002/jcp.1030420103] for sectioning biological specimens.   
 
 
 Ultramicrotomy methods have improved significantly since the 1950s. 
 A critical advancement was Humberto Fernández-Morán's development of the diamond knife in 1953-1955, which offered better sharpness and durability than glass knives and could section harder materials [@https://doi.org/bzp3r6]. 
 Fernández-Morán also introduced cryo-ultramicrotomy in 1952, which preserved samples at low temperatures without chemical fixatives. 
-The microtomes themselves evolved from simple  mechanical systems in the 1950s to modern, digitally-controlled systems with automated sectioning and greater precision and reproducibility [@reid1975practical; @https://doi.org/10.1007/978-1-4419-9244-4_5]. 
+The microtomes themselves evolved from simple mechanical systems in the 1950s to modern, digitally-controlled systems with automated sectioning and greater precision and reproducibility [@reid1975practical; @https://doi.org/10.1007/978-1-4419-9244-4_5]. 
 Ultramicrotomy remains essential for ultrastructural investigations requiring high spatial resolution with minimal preparation-induced artifacts.
 Ultramicrotomy applications have expanded to include polymers, semiconductor cross-sectioning, nanoparticle distribution analysis, and coating examination. 
 Geological and astromaterial applications include mineral composition and structure, organic-mineral composites, and radiation tracks, and coordinated studies on serial slices with different instruments. 
@@ -34,7 +34,7 @@ In order to use the ultramicrotome to section samples, the samples must be robus
 
 The optimal embedding material depends on the sample properties and which specific analyses are planned.
 Traditional embedding protocols employ epoxy resins that work well for conventional light optical studies, and transmission electron microscope studies under low beam current densities in moderate vacuum conditions.
-Epoxy resins offer  excellent sectioning properties and compatibility with standard staining protocols [@https://doi.org/10.1083/jcb.9.2.409] for low Z materials, and are also generally stable for storage for longitudinal studies.
-However, epoxy resins can be problematic for polymer composite samples due to  potential chemical contamination, thermal degradation during curing, and difficulty sectioning heterogeneous mineral assemblages [@https://doi.org/10.3390/life10080135; @plummer2025ultramicrotomy].
+Epoxy resins offer excellent sectioning properties and compatibility with standard staining protocols [@https://doi.org/10.1083/jcb.9.2.409] for low Z materials, and are also generally stable for storage for longitudinal studies.
+However, epoxy resins can be problematic for polymer composite samples due to potential chemical contamination, thermal degradation during curing, and difficulty sectioning heterogeneous mineral assemblages [@https://doi.org/10.3390/life10080135; @plummer2025ultramicrotomy].
 Epoxy resins are generally not robust to the probe current densities widely used in conventional field emission and aberration-corrected scanning transmission electron microscopes [@https://doi.org/10.1016/j.micron.2004.02.003; @https://doi.org/10.1017/S1431927608080902]. 
-Sulfur is a useful alternative to epoxy embedding because it provides the necessary mechanical robustness for the microtomy, and can be sublimated at low temperature after the section to leave the bare sample section. This eliminates the vacuum degradation from the epoxy outgassing  in the electron microscope, sample contamination from volatilization and redeposition of the epoxy hydrocarbons and beam-induced shrinkage of the epoxy leading to sample mechanical instability in the microscope. This study presents a comprehensive sulfur-embedding protocol specifically optimized for preparing ultrathin sections (50-100 nm in thickness) particles with varied composition. We evaluate sectioning quality, sample preservation, and compatibility with advanced microscopic and spectroscopic techniques without conventional epoxy embedding methods.
+Sulfur is a useful alternative to epoxy embedding because it provides the necessary mechanical robustness for the microtomy and can be sublimated at low temperature after sectioning to leave the bare sample section. This eliminates vacuum degradation from epoxy outgassing in the electron microscope, sample contamination from volatilization and redeposition of epoxy hydrocarbons, and beam-induced shrinkage of the epoxy leading to sample mechanical instability in the microscope. This study presents a comprehensive sulfur-embedding protocol specifically optimized for preparing ultrathin sections (50-100 nm in thickness) of particles with varied composition. We evaluate sectioning quality, sample preservation, and compatibility with advanced microscopic and spectroscopic techniques without conventional epoxy embedding methods.

01_instrumentation.md

@@ -3,7 +3,7 @@ title: Instrumentation
 ---
 
 ## Ultramicrotome
-The essential components of a microtome are: a sample mounted in/on a bullet of epoxy; a chuck to secure the bullet; a knife blade; a mechanism to advance the sample towards the knife, and raise and lower the sample vertically at the knife edge.
+The essential components of a microtome are: a sample mounted in or on a bullet of epoxy; a chuck to secure the bullet; a knife blade; a mechanism to advance the sample towards the knife, and raise and lower the sample vertically at the knife edge.
 Automated ultramicrotomes advance the specimen arm holding the embedded sample block towards the cutting knife edge with precision and reproducibility. 
 The knife stage maintains the cutting edge at adjustable clearance angles, typically 6°, optimized for the specimen's properties. A stereomicroscope with appropriate illumination permits real-time monitoring of the sectioning process. The sample slices float off of the knife into a bath, usually filled with water.
 Either glass or diamond knives can be used, depending on the materials being cut and the desired thickness. 
@@ -27,7 +27,7 @@ The mechanical system controls the sectioning interval and determines section th
 
 ### Knife and Knife Holder: 
 The ultramicrotome uses either a glass knife for initial rough cuts or diamond knife for most ultra-thin sectioning. 
-Diamond knives come in different angles, typically 35°or 45°, with edge lengths ranging from 1 to 7 mm depending on the application. 
+Diamond knives come in different angles, typically 35° or 45°, with edge lengths ranging from 1 to 7 mm depending on the application. 
 The knife has an attached boat or trough that holds water, allowing the sections to float as they are cut.
 
 :::{figure} ./figures/fig_3.png
@@ -75,4 +75,4 @@ The base platform holds and positions the sample holder, allowing for precise tr
 :::{figure} ./figures/fig_6b.png
 :name: stage_mounted
 **Custom removable stage for sulfur embedding.** A specialized stage was fabricated with increased mass for vibration dampening, thermal isolation to prevent external heat transfer, and precise leveling mechanisms. Isolation mounts decouple the working surface from building vibrations and mechanical disturbances, ensuring stable conditions during the critical sulfur solidification phase and precise specimen positioning.
-:::
+:::