NanoSIMS_depth-profiles_O- & Cs+ beam

Data for Figures 3 and S6 in paper: "Elucidating Heterogeneous Iron Biomineralization Patterns in a Denitrifying As(III)-Oxidizing Bacterium: Implications for Arsenic Immobilization"<br>Single Acidovorax sp. ST3 cells (7 days incubation) were selected for depth profiling. Both Cs⁺ and O^- were used as primary ions and the selected areas were not implanted prior to starting the analysis (to preserve and keep the biomineral coating on the cells intact). Image raster sizes were 3-7 µm width. Spatial resolution was achieved by using D1=4 or 5 (beam size=120-100 nm). Pixel sizes were 128 x 128 or 256 x 256, and dwell time varied from 5,000-20,000 µs px^-1. 50-170 planes were collected, and the scanning was stopped when the ¹²C¹⁴N or ⁵⁶Fe⁺signal disappeared. The data was processed using the L’image software (Larry Nittler, Carnegie Institution of Washington) and the plugin OpenMIMS for ImageJ (www.nrims.harvard.edu). 3D reconstructions of the depth profiles were generated using the Thermo Scientific™ Avizo™ Software 9.7.0. Stack data of the negative secondary ions¹²C^-, ⁵⁶Fe¹⁶O^- and ⁷⁵As^-, and the positive secondary ions ²³Na⁺, ⁵⁶Fe⁺, and ⁷⁵As⁺, were first extracted in ImageJ and saved as “.raw” format files, which were loaded into Avizo™. The Z depth was compressed to 15-20 %. The ¹²C^- and ²³Na⁺signals were smoothed over 2-3 pixels. The commands “generate surface” and “show surface” were used sequentially, and the “transparent” display with a transparency of 80 % was selected. ⁵⁶Fe⁺ and ⁵⁶Fe¹⁶O^- signals were smoothed to 2 pixels and displayed as “shaded”. The ⁷⁵As^+/-ion counts were smoothed to 1 pixel.<br>Four depth profile files are presented, including the .im raw nanoSIMS files, extracted ⁷⁵As^+/-, ⁵⁶Fe¹⁶O^-/⁵⁶Fe⁺, ¹²C/²³Na counts as .raw format (ready to load into AVIZO), and complementary image and videos of the 3D reconstructions for each depth profile (jpg and mpg formats).

本数据集为论文《反硝化三价砷氧化细菌中非均一铁生物矿化模式解析：对砷固定的启示》中图3与补充图S6所用数据。
选取培养7天的单一嗜酸菌属（Acidovorax sp.）ST3菌株细胞进行深度剖面分析。实验采用铯离子（Cs⁺）与氧离子（O⁻）作为一次离子，分析开始前未对选定区域进行预注入处理，以完整保留细胞表面的生物矿化涂层。
图像扫描光栅尺寸宽度为3~7 μm。空间分辨率通过设置D1=4或5实现，对应束斑尺寸为120~100 nm。像素尺寸设为128×128或256×256，驻留时间范围为5000~20000 μs·px⁻¹。
共采集50~170层切片，当¹²C¹⁴N或⁵⁶Fe⁺信号消失时停止扫描。
数据使用L’image软件（华盛顿卡内基研究所Larry Nittler开发）以及ImageJ插件OpenMIMS（网址：www.nrims.harvard.edu）进行处理。
采用赛默飞世尔科技™ Avizo™ 9.7.0软件生成深度剖面的三维重建结果。
首先在ImageJ中提取负二次离子¹²C⁻、⁵⁶Fe¹⁶O⁻与⁷⁵As⁻，以及正二次离子²³Na⁺、⁵⁶Fe⁺与⁷⁵As⁺的堆叠数据，并保存为.raw格式文件，随后将其导入Avizo™中。
将Z轴深度压缩至15%~20%。
对¹²C⁻与²³Na⁺信号进行2~3像素的平滑处理。
依次执行"生成表面"与"显示表面"命令，并选择透明度为80%的"透明"显示模式。
对⁵⁶Fe⁺与⁵⁶Fe¹⁶O⁻信号进行2像素平滑处理，并以"着色"模式显示。
对⁷⁵As⁺/⁻的离子计数进行1像素平滑处理。
本次共提供4个深度剖面文件，包括.nanoSIMS原始.im文件、提取得到的⁷⁵As⁺/⁻、⁵⁶Fe¹⁶O⁻/⁵⁶Fe⁺、¹²C/²³Na计数的.raw格式文件（可直接导入Avizo™），以及每个深度剖面三维重建结果的配套图像与视频文件（格式分别为jpg与mpg）。