This readme.txt file was generated on <20230426> by Recommended citation for the data: Wei, Guanju; Yang, Judy. (2023). Experimental data of biofilm development experiments under fluctuating flow conditions taken and processed at SAFL in 2022. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/jwgn-4078. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Experimental data of biofilm development experiments under fluctuating flow conditions (43 GB) 2. Author Information Principal Investigator Contact Information Name: Guanju Wei Institution: Saint Anthony Falls Laboratory, University of Minnesota Address: 2 3rd Ave SE, Minneapolis, MN 55414 Email: wei00235@umn.edu ORCID: 0000-0001-5511-9242 Associate or Co-investigator Contact Information Name: Judy Yang Institution: Saint Anthony Falls Laboratory, University of Minnesota Address: 2 3rd Ave SE, Minneapolis, MN 55414 Email: judyyang@umn.edu ORCID: 0000-0001-6272-1266 3. Date published or finalized for release: 20230426 4. Date of data collection (single date, range, approximate date) 20220712-20221014 5. Geographic location of data collection (where was data collected?): Saint Anthony Falls Laboratory, University of Minnesota 6. Information about funding sources that supported the collection of the data: This study was supported by National Science Foundation Career Award EAR 2236497 and MnDRIVE Environment at the University of Minnesota. Portions of this work were conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nanotechnology Coordinated Infrastructure (NNCI) under Award Number ECCS-2025124. 7. Overview of the data (abstract): This dataset consists of the Matlab codes, experimental data, and raw images of the biofilm development experiments under fluctuating flow conditions. They are all collected in the Saint Anthony Falls Laboratory at the University of Minnesota. The codes are used for processing the raw images to calculate the biofilm thickness and biofilm area coverage. The experimental data file contains the data after processing. The image file contains the raw images collected during the experiments using the Nikon confocal microscope. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Manuscript in preparation 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Matlab codes (folder) Short description: This folder contains Matlab codes files. They are used to calculate the biofilm thickness and biofilm area coverage based on the color difference. Matlab R2021b was used. B. Filename: Data (folder) Short description: This folder contains two files: (1) Biofilm thickness.xlsx, this file contain the data of biofilm thickness. (2) Ripple area.xlsx, this file contain the data of biofilm area coverage. Each file has 4 worksheets. C. Filename: Raw images (Steady.zip, Low frequency.zip, Middle frequency.zip, High frequency.zip) Short description: This file contains all the raw images collected by the Nikon confocal microscope. It contains four subfolders represents four flow conditions: steady, low frequency, middle frequency and high frequency. Each folder contains three replicate measurements (two for steady condition). 2. Relationship between files: The raw images folder contains the raw images collected using Nikon confocal microscope. The Matlab codes are used for processing these raw images to calculate the biofilm thickness and biofilm area coverage. The data folder contains the data after processing. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: During the biofilm development experiments, the microfluidic channels were visualized using a Nikon C2+ confocal laser scanning microscope (CLSM) with 0.31 μm-horizontal resolution and 0.82 μm-vertical resolution. The wavelength of the laser used here is 488 nm. Biofilms in the entire microfluidic channel were scanned piece by piece with each image 2048 by 2048 pixels. These images were combined into a single image using the Large-Image functions of Nikon NIS-Elements software. Biofilms over the channel depth were scanned at several vertical positions at 0.5 μm vertical resolution using the Z-Stack function of the Nikon NIS-Elements software. Cross-sectional images of biofilms at the middle depth of the channel were used in our analysis. The objective magnification was 10-X and 20-X. During the experiment, the images were scanned at 10- to 30-minute intervals over 48 hours and saved on an HP-Z4-G4 workstation. 2. Methods for processing the data: We scanned the biofilms in the microfluidic channel in three-dimensional space using the Z-stack function of the Nikon confocal microscope. These confocal images show that the ripple-like biofilms only occupied the top surface of the channel, while biofilms on the sidewalls occupied the whole channel depth. Consequently, the light intensity of the pixel occupied by sidewall biofilms was darker than that of regions occupied by ripple-like biofilms on the top surface. To quantify the biofilm thickness of the sidewall biofilms and the area coverage of ripple-like biofilms, we employed Image-J and MATLAB and followed the subsequent steps. Since the sidewall biofilms and top surface biofilms had distinct color differences (the color intensity distribution had two-peak distribution), we converted the grayscale images into binary images using Otsu’s method and applied this threshold to subtract the biofilm images from the background image (the image at the beginning of the experiments). After identifying the regions occupied by biofilms on the sidewalls, we computed the average biofilm thickness by dividing the total biofilm area by the length of the field of view (4 mm). Regarding the ripple-like biofilms formed on the top PDMS surfaces, since the ripple-like structures only occupied a portion of the space of the whole channel and had little color difference with the background; the color intensity distribution had only one peak and was not suitable for using Otsu’s method. Therefore, we manually determined the threshold by comparing the pixel intensity between the light intensity of the ripple-like biofilms and the background using Image-J and employed this threshold to binarize all the images. Subsequently, we calculated the biofilm area coverage by dividing the total biofilm area by the entire area. 3. Instrument- or software-specific information needed to interpret the data: Image-J, Matlab, Excel 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: The Pseudomonas putida bacterial solution was placed in an incubator with 200 rpm shaking rate at 30 ℃. 6. Describe any quality-assurance procedures performed on the data: The data are shown as mean ± standard error. The mean value was calculated from three replicates. The error bars indicate standard error of three replicates. At least one biological replicate was conducted for all the cases. 7. People involved with sample collection, processing, analysis and/or submission: Guanju Wei (sample collection, processing, analysis, submission) Judy Yang (analysis, submission) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Biofilm thickness.xlsx] in Data.zip ----------------------------------------- 1. Number of variables: 7 2. Number of cases/rows: 146 3. Missing data codes: N/A 4. Variable List A. Name: