FDTD simulation data for Optical Diffraction Tomography

This dataset contains 2D and 3D complex field sinograms for optical diffraction tomography created with finite-difference time domain simulations using Meep (http://ab-initio.mit.edu/wiki/index.php?title=Meep). The entire complex electric field data from the simulations would have amounted to &gt;2TB of data which is not easy to share and also contain a lot of redundant and uninteresting (for tomography at least) information. Most of these data were used in the ODTbrain paper (https://dx.doi.org/10.1186/s12859-015-0764-0). <br> <b>Data Structure</b> Each dataset is an HDF5 file (https://www.hdfgroup.org) that contains the simulation structure (the cell phantom), a background field (simulation without phantom), and a field for each rotational position of the phantom (sinogram). The fields are slices through the complex electrical field in the original simulation volume behind the phantom at the end of the simulation (supposedly steady state). The slice position is written as the HDF5 attribute “extraction focus distance [px]”. The slice position is important for the reconstruction, because the fields must be numerically refocused to the center of the simulation volume before reconstruction. The perfectly matched layer (PML) has already been cropped from the fields. Alongside each field, the source code of the Meep simulation and the standard-output of the compiled simulation are stored. You can also find the simulation templates in the ODTbrain repository at https://github.com/RI-imaging/ODTbrain/tree/master/misc. I recommend you to explore the files using HDFView (https://www.hdfgroup.org/downloads/hdfview/). <br> <b>Naming Scheme</b> I adopted the naming scheme of the original simulations. - The first part of the file name determines the dimension of the simulation. The larger “phantom_3d” files contain the 3D simulation sinograms. - “A” is the total number of angles for which simulations were performed. - “R” is the resolution (number of pixels per wavelength). - “T” is the total number of simulation steps performed. - “Nmed” is the refractive index (RI) of the medium surrounding the cell phantom. - “Ncyt” is the RI of the phantom’s cytoplasm. - “Nnuc” is the RI of the phantom’s nucleus. - “Nleo” is the RI of the phantom’s nucleolus. The final part of the file name indicates to which type of study the simulation belongs: - “angles”: varying the total number of acquisition angles - “step-count”: varying the total number of time steps - “refractive-index”: varying the internal RI values of the cell phantom - “size”: varying the size of the phantom <br> <b>Getting Started</b> I added two Python scripts “recon_2d.py” and “recon_3d.py” (tested with Python 3.9 on Ubuntu 22.04) that will allow you to obtain RI reconstructions from the 2D and 3D sinograms. For this to work, you will have to install the Python libraries imported in those scripts. Note that for the 3D data you can also use the graphical tool CellReel (https://github.com/RI-imaging/CellReel).<br>本数据集包含用于光学衍射层析成像（optical diffraction tomography）的二维与三维复场正弦图（sinogram），这些数据通过采用Meep的时域有限差分（finite-difference time domain, FDTD）仿真生成，相关说明链接为http://ab-initio.mit.edu/wiki/index.php?title=Meep。 仿真产出的全部复电场数据总量将超过2TB，不仅难以共享，还包含大量冗余且（至少对于层析成像而言）无关的信息。本数据集的绝大多数数据已在ODTbrain相关论文（https://dx.doi.org/10.1186/s12859-015-0764-0）中使用。 <b>数据结构</b> 每个数据集均为HDF5格式文件（https://www.hdfgroup.org），其中包含仿真结构（细胞体模）、背景场（无体模的仿真结果）以及对应体模每个旋转位置的复场（即正弦图）。此处的复场为仿真结束时（此时场已趋于稳态），原仿真体中体模后方区域的复电场切片。切片位置以HDF5属性"extraction focus distance [px]（提取焦距[像素]）"的形式存储。切片位置对于重建过程至关重要，因为在进行重建前，需通过数值计算将复场重聚焦至仿真体的中心位置。完美匹配层（perfectly matched layer, PML）已从复场中移除。每个复场文件旁均存储了Meep仿真的源代码与编译后仿真程序的标准输出日志。仿真模板可在ODTbrain仓库的对应路径（https://github.com/RI-imaging/ODTbrain/tree/master/misc）中获取。建议使用HDFView（https://www.hdfgroup.org/downloads/hdfview/）浏览数据集文件。 <b>命名规则</b> 本数据集沿用了原始仿真的命名规则： - 文件名的首段用于标识仿真的维度，其中带"phantom_3d"标识的文件包含三维仿真正弦图； - 字段"A"代表仿真执行时的总采集角度数； - 字段"R"代表分辨率（即每波长对应的像素数）； - 字段"T"代表仿真执行的总步数； - 字段"Nmed"代表细胞体模周围介质的折射率（refractive index, RI）； - 字段"Ncyt"代表体模细胞质的折射率； - 字段"Nnuc"代表体模细胞核的折射率； - 字段"Nleo"代表体模核仁的折射率。 文件名的末尾段用于标识该仿真所属的研究类型： - "angles"：调整采集总角度数的仿真； - "step-count"：调整总仿真时间步数的仿真； - "refractive-index"：调整细胞体模内部折射率参数的仿真； - "size"：调整体模尺寸的仿真。 <b>快速上手</b> 本数据集附带两个Python脚本"recon_2d.py"与"recon_3d.py"（已在Ubuntu 22.04环境下基于Python 3.9完成测试），可用于从二维与三维正弦图中获取折射率重建结果。运行脚本前需安装脚本中导入的Python依赖库。需注意，针对三维数据，也可使用图形化工具CellReel（https://github.com/RI-imaging/CellReel）进行处理。