Particle area analysis of crystals formed via urease-dependent, microbially induced calcite precipitation (MICP) in a microfluidic cell

Note: This dataset belongs to the master’s thesis “Investigation of urease-dependent, microbially induced calcite precipitation by Sporosarcina pasteurii” (see below). The chapters of interest regarding this dataset are chapter 2.7 (method), 3.5 (results) and 4.5 (discussion). Folder content: This dataset is stored in three separate folders. The results of the two experiments are stored in the folders “1_5M” and "3M". The name of these folders represent the concentration of urea and calcium chloride (CaCl2) in the different cementation solutions (1,5 M or 3 M respectively). These folders contain several subfolders (see point "Directory"). The several scripts, which were used to analyze the particle area of five crystals per experiment, are stored in the folder "scripts". For a short description of their effects see the point "Used scripts". Directory: 1_5M (concentration of the used cementation solution) 1_Rohbilder (contains raw images) 2_Rohbilder_bearbeitet (results of "preprocessing.ijm"; used for particle analysis) 3_Partikel1 (analysis of crystal 1) Bilder (results of "particle_analysis.ijm" and "postprocessing1.ijm") [date]_[time]_[number]_Kristall.tif (section of the initial images with the crystal) [date]_[time]_[number]_markiert.tif (initial images marked with the position of the crystal) [date]_[time]_[number]_Umrisse.tif (section of the initial images with the detected areas) Ergebnisse (contains text files with the values of every detected area; results of "particle_analysis.ijm") flaechen1.txt (contains the measured areas of the crystal, first two hours; results of "auswertung_flaeche.pl") flaechen2.txt (contains the measured areas of the crystal, last two hours; results of "auswertung_flaeche.pl") 3_Partikel2 (analysis of crystal 2; same folder structure as "3_Partikel1") 3_Partikel3 (analysis of crystal 3; same folder structure as "3_Partikel1") 3_Partikel4 (analysis of crystal 4; same folder structure as "3_Partikel1") 3_Partikel5 (analysis of crystal 5; same folder structure as "3_Partikel1") 4_Bilder_markiert (initial images marked with the positions of the five analyzed crystals) 3M (concentration of the used cementation solution; same folder structure as "1_5M") Used scripts: preprocessing.ijm: sets a predefined scale cuts out a part of the images (input from the user) turns cutouts 180° saves cutouts as separate images particle_analysis.ijm: cuts out a part of the images (input from the user; results of "preprocessing.ijm") uses a range of gray values to identify the crystal areas (input from the user) measures the areas of connected pixels with gray values inside the defined range marks the position of the analyzed crystals in the initial images and inserts a scale bar saves the cutouts with the crystals, the cutouts with the detected areas and the initial images with the marked positions as separate images saves the measured areas in text files postprocessing1.ijm: inserts a scale bar in the cutouts (results from "particle_analysis.ijm") overrides the respective images postprocessing2.ijm: marks the position of the five analyzed crystals in the initial images (results of "preprocessing.ijm") inserts a scale bar saves the images with the marked positions and scale bar as separate images auswertung_flaeche.pl: identifies the biggest measured particle area in every text file (results of "particle_analysis.ijm") saves the biggest particle areas in two text files (first and last two hours)

注：本数据集属于硕士学位论文《探究Sporosarcina pasteurii诱导的脲酶依赖性微生物诱导碳酸钙沉淀的研究》（详见下文）。与该数据集相关的章节包括第2.7节（方法）、第3.5节（结果）和第4.5节（讨论）。文件夹内容：本数据集存储于三个独立的文件夹中。两次实验的结果分别存储在“1_5M”和“3M”文件夹中。这些文件夹的名称代表不同固化溶液中尿素和氯化钙（CaCl2）的浓度（分别为1,5 M或3 M）。这些文件夹包含多个子文件夹（参见“目录”部分）。分析每个实验中五个晶体颗粒面积的脚本存储在“scripts”文件夹中。关于其效果的简要描述见“使用的脚本”部分。目录：1_5M（所使用固化溶液的浓度）1_Rohbilder（包含原始图像）2_Rohbilder_bearbeitet（“preprocessing.ijm”的处理结果；用于颗粒分析）3_Partikel1（晶体1的分析；与“3_Partikel1”文件夹结构相同）Bilder（“particle_analysis.ijm”和“postprocessing1.ijm”的处理结果）[日期]_[时间]_[编号]_Kristall.tif（初始图像中晶体的截面）[日期]_[时间]_[编号]_markiert.tif（标记晶体位置的初始图像）[日期]_[时间]_[编号]_Umrisse.tif（初始图像中检测到的区域的截面）Ergebnisse（包含每个检测区域值的文本文件；为“particle_analysis.ijm”的结果）flaechen1.txt（包含晶体测量的面积，前两小时；为“auswertung_flaeche.pl”的结果）flaechen2.txt（包含晶体测量的面积，最后两小时；为“auswertung_flaeche.pl”的结果）3_Partikel2（晶体2的分析；与“3_Partikel1”文件夹结构相同）3_Partikel3（晶体3的分析；与“3_Partikel1”文件夹结构相同）3_Partikel4（晶体4的分析；与“3_Partikel1”文件夹结构相同）3_Partikel5（晶体5的分析；与“3_Partikel1”文件夹结构相同）4_Bilder_markiert（标记五个分析晶体的初始图像）3M（所使用固化溶液的浓度；与“1_5M”文件夹结构相同）使用的脚本：preprocessing.ijm：设定预定义的比例尺，裁剪图像的一部分（用户输入）将裁剪的部分旋转180°，保存为单独的图像particle_analysis.ijm：裁剪图像的一部分（用户输入；为“preprocessing.ijm”的结果）使用一系列灰度值以识别晶体区域（用户输入）测量灰度值在定义范围内相连像素的面积标记分析晶体的位置，并在初始图像中插入比例尺将含有晶体的裁剪、含有检测区域的裁剪以及标记位置的初始图像保存为单独的图像将测量的面积保存到文本文件中postprocessing1.ijm：在裁剪中插入比例尺（为“particle_analysis.ijm”的结果）覆盖相应的图像postprocessing2.ijm：在初始图像中标记五个分析晶体的位置（为“preprocessing.ijm”的结果）插入比例尺，将带有标记位置和比例尺的图像保存为单独的图像auswertung_flaeche.pl：在每篇文本文件中识别最大的测量颗粒面积将最大的颗粒面积保存到两个文本文件中（前两小时和最后两小时）