DOI: 10.18419/darus-3298
title: Particle area analysis of crystals formed via urease-dependent, microbially induced calcite precipitation (MICP) in a microfluidic cell

description: &lt;p&gt;
 &lt;b&gt;Note:&lt;/b&gt;&lt;br&gt;
 This dataset belongs to the master’s thesis “Investigation of urease-dependent, microbially induced calcite precipitation by &lt;i&gt;Sporosarcina pasteurii&lt;/i&gt;” (see below). The chapters of interest regarding this dataset are chapter 2.7 (method), 3.5 (results) and 4.5 (discussion). 
&lt;/p&gt;
&lt;p&gt;
 &lt;b&gt;Folder content:&lt;/b&gt;&lt;br&gt;
 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 (CaCl&lt;sub&gt;2&lt;/sub&gt;) 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". 
&lt;/p&gt;
&lt;p&gt;
 &lt;b&gt;Directory:&lt;/b&gt;&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;1_5M (concentration of the used cementation solution)&lt;/li&gt;
 &lt;ul&gt;
 &lt;li&gt;1_Rohbilder (contains raw images)&lt;/li&gt;
 &lt;li&gt;2_Rohbilder_bearbeitet (results of "preprocessing.ijm"; used for particle analysis)&lt;/li&gt;
 &lt;li&gt;3_Partikel1 (analysis of crystal 1)&lt;/li&gt;
 &lt;ul&gt;
 &lt;li&gt;Bilder (results of "particle_analysis.ijm" and "postprocessing1.ijm")&lt;/li&gt;
 &lt;ul&gt;
 &lt;li&gt;[date]_[time]_[number]_Kristall.tif (section of the initial images with the crystal)&lt;/li&gt;
 &lt;li&gt;[date]_[time]_[number]_markiert.tif (initial images marked with the position of the crystal)&lt;/li&gt;
 &lt;li&gt;[date]_[time]_[number]_Umrisse.tif (section of the initial images with the detected areas)&lt;/li&gt;
 &lt;/ul&gt;
 &lt;li&gt;Ergebnisse (contains text files with the values of every detected area; results of "particle_analysis.ijm")&lt;/li&gt;
 &lt;li&gt;flaechen1.txt (contains the measured areas of the crystal, first two hours; results of "auswertung_flaeche.pl")&lt;/li&gt;
 &lt;li&gt;flaechen2.txt (contains the measured areas of the crystal, last two hours; results of "auswertung_flaeche.pl")&lt;/li&gt;
 &lt;/ul&gt;
 &lt;li&gt;3_Partikel2 (analysis of crystal 2; same folder structure as "3_Partikel1")&lt;/li&gt;
 &lt;li&gt;3_Partikel3 (analysis of crystal 3; same folder structure as "3_Partikel1")&lt;/li&gt;
 &lt;li&gt;3_Partikel4 (analysis of crystal 4; same folder structure as "3_Partikel1")&lt;/li&gt;
 &lt;li&gt;3_Partikel5 (analysis of crystal 5; same folder structure as "3_Partikel1")&lt;/li&gt;
 &lt;li&gt;4_Bilder_markiert (initial images marked with the positions of the five analyzed crystals)&lt;/li&gt;
 &lt;/ul&gt;
 &lt;li&gt;3M (concentration of the used cementation solution; same folder structure as "1_5M")&lt;/li&gt;
 &lt;/ul&gt;
&lt;/p&gt;
&lt;p&gt;
 &lt;b&gt;Used scripts:&lt;/b&gt;&lt;br&gt;
 preprocessing.ijm:&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;sets a predefined scale&lt;/li&gt;
 &lt;li&gt;cuts out a part of the images (input from the user)&lt;/li&gt;
 &lt;li&gt;turns cutouts 180°&lt;/li&gt;
 &lt;li&gt;saves cutouts as separate images&lt;/li&gt;
 &lt;/ul&gt;
 particle_analysis.ijm:&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;cuts out a part of the images (input from the user; results of "preprocessing.ijm")&lt;/li&gt;
 &lt;li&gt;uses a range of gray values to identify the crystal areas (input from the user)&lt;/li&gt;
 &lt;li&gt;measures the areas of connected pixels with gray values inside the defined range&lt;/li&gt;
 &lt;li&gt;marks the position of the analyzed crystals in the initial images and inserts a scale bar&lt;/li&gt;
 &lt;li&gt;saves the cutouts with the crystals, the cutouts with the detected areas and the initial images with the marked positions as separate images&lt;/li&gt;
 &lt;li&gt;saves the measured areas in text files&lt;/li&gt;
 &lt;/ul&gt;
 postprocessing1.ijm:&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;inserts a scale bar in the cutouts (results from "particle_analysis.ijm")&lt;/li&gt;
 &lt;li&gt;overrides the respective images&lt;/li&gt;
 &lt;/ul&gt;
 postprocessing2.ijm:&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;marks the position of the five analyzed crystals in the initial images (results of "preprocessing.ijm")&lt;/li&gt;
 &lt;li&gt;inserts a scale bar&lt;/li&gt;
 &lt;li&gt;saves the images with the marked positions and scale bar as separate images&lt;/li&gt;
 &lt;/ul&gt;
 auswertung_flaeche.pl:&lt;br&gt;
 &lt;ul&gt;
 &lt;li&gt;identifies the biggest measured particle area in every text file (results of "particle_analysis.ijm")&lt;/li&gt;
 &lt;li&gt;saves the biggest particle areas in two text files (first and last two hours)&lt;/li&gt;
 &lt;/ul&gt;
&lt;/p&gt;