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).

本数据集对应论文《反硝化三价砷（As(III)）氧化细菌中铁非均一生成矿物模式的阐明：对砷固定的启示》（*Elucidating Heterogeneous Iron Biomineralization Patterns in a Denitrifying As(III)-Oxidizing Bacterium: Implications for Arsenic Immobilization*）中的图3与补充图S6。
实验选取培养7天的单株嗜酸食酸菌（*Acidovorax* sp.）ST3细胞，用于深度剖面分析（depth profiling）。分别以铯阳离子（Cs⁺）与氧阴离子（O⁻）作为一次离子，且分析前未对选定区域进行离子注入，以完整保留细胞表面的生物矿物涂层。图像光栅扫描视野的宽度为3~7 μm；通过设置参数D1=4或5获得空间分辨率，对应束斑尺寸为120~100 nm。像素尺寸设为128×128或256×256，每像素驻留时间为5000~20000微秒·像素⁻¹。共采集50~170层扫描平面，当¹²C¹⁴N⁺或⁵⁶Fe⁺信号消失时停止扫描。
数据处理采用L'image软件（Larry Nittler，华盛顿卡内基研究所）以及适配ImageJ软件的OpenMIMS插件（网址：www.nrims.harvard.edu）。深度剖面的三维重构使用赛默飞世尔科技（Thermo Scientific™）Avizo™ 9.7.0版软件完成：首先在ImageJ软件中提取负二次离子（negative secondary ions）¹²C⁻、⁵⁶Fe¹⁶O⁻与⁷⁵As⁻，以及正二次离子（positive secondary ions）²³Na⁺、⁵⁶Fe⁺与⁷⁵As⁺的信号数据，保存为.raw格式文件后导入Avizo™软件；将Z轴深度压缩至原尺寸的15%~20%；对¹²C⁻与²³Na⁺信号以2~3像素为窗口进行平滑处理，依次执行"generate surface"与"show surface"命令，并选择透明度为80%的透明显示模式；对⁵⁶Fe⁺与⁵⁶Fe¹⁶O⁻信号以2像素为窗口进行平滑处理，采用阴影渲染模式展示；对⁷⁵As⁺/⁻的离子计数数据以1像素为窗口进行平滑处理。
本次公开的深度剖面数据文件共四类：包含.im格式的原始纳米二次离子质谱（nanoSIMS）文件、以.raw格式保存的提取得到的⁷⁵As⁺/⁻、⁵⁶Fe¹⁶O⁻/⁵⁶Fe⁺、¹²C与²³Na⁺离子计数文件（可直接导入Avizo™软件），以及各深度剖面三维重构的配套图像与视频文件（格式分别为jpg与mpg）。