Analyzed Image Dataset of Laser-Assisted Biofilm Removal in Periodontal Pocket Models

This file (ReadMe) was created on 2026-05-05 by MARKO VOLK

-------------------GENERAL INFORMATION-------------------

Dataset title: Analyzed Image Dataset of Laser-Assisted Biofilm Removal in Periodontal Pocket Models

Author / Principal Investigator InformationName: Marko VolkORCID: /Institution: Department of Microbiology, Biotechnical Faculty, University of Ljubljana, SloveniaAddress: Večna pot 111, 1000 LjubljanaEmail: [e-mail]

Role in this dataset: Principal investigator

Data collection period: 2022-10-01 to 2025-10-01

Geographic location of data collection: Biotechnical Faculty

Funding sources/programs/projects: ARRS project L7-3186, and funding from national programs P4-0116 and P2-0392

-----------------------------SHARING / ACCESS INFORMATION-----------------------------

Licenses/restrictions: CC BY 4.0

Publications associated with this dataset:

Volk M., Molan K., Šavli D., Terlep S., Levičnik-Höfferle Š., Gašpirc B., Lukač M., Jezeršek M., Stopar D. 2024. Biofilm removal from difficult-to-reach places via secondary cavitation within a constrained geometry mimicking a Periodontal/Peri-Implant pocket. Ultrasonics Sonochemistry, 104: 106832, https://doi.org/10.1016/j.ultsonch.2024.106832

Volk M., Šavli D., Molan K., Terlep S., Levičnik-Höfferle Š., Trost M., Gašpirc B., Lukač M., Jezeršek M., Stopar D. 2025. Er:YAG laser biofilm removal from zero-gap periodontal/peri-implant model system mimicking clinical attachment loss. Journal of Biomedical Optics, 30, 2: 025002, https://doi.org/10.1117/1.JBO.30.2.025002

Šavli D., Volk M., Molan K., Terlep S., Levičnik-Höfferle Š., Babnik A., Trost M., Gašpirc B., Lukač M., Stopar D., Jezeršek M. 2025. The effect of surface roughness on the Er:YAG laser-induced photoacoustic removal of bacteria in zero-gap periodontal/peri-implant pocket model. Ultrasonics Sonochemistry, 120: 107458, https://doi.org/10.1016/j.ultsonch.2025.107458

Links to other publicly accessible data locations: /Links to related datasets: /

Were the data derived from another source? NoIf yes, specify the source(s):

---------------------------DATA AND FILE OVERVIEW---------------------------

File list:-wedge-shaped model cleaning.xlsxThis file contains processed data from microscopic images of biofilm-covered surfaces in a wedge-shaped model system. The percentage of biofilm surface removed after laser treatment is reported. Columns represent different replicates, while rows represent different measurement positions. The last two columns show the mean and standard error. Below the table, the average removed biofilm surface is presented for the upper, middle, and lower regions of the model system. -narrow-gap model cleaning.xlsxThis file contains processed data from microscopic images of biofilm-covered surfaces in a narrow-gap model system. The percentage of biofilm surface removed after laser treatment is reported. Columns represent different replicates, while rows represent different measurement positions. The last two columns show the mean and standard error. Measurement conditions are specified above the table.

Relationships between files (if relevant):

Additional related data not included in this dataset: /

Are there multiple versions of the dataset? NoIf yes, specify updated file name: /Date of update: 2026-05-05Reason for update: The file was edited to improve clarity and usability

-----------------------METHODOLOGICAL INFORMATION-----------------------

Methods used for data collection:Biofilms were imaged using light microscopy and confocal fluorescence microscopy. The acquired images were analyzed using ImageJ and BiofilmQ software.

Data processing methods:

ImageJ – surface coverage determinationMicrosoft Excel – basic calculationsIBM SPSS – Mann–Whitney U test

Software used: IBM SPSS Statistics 23, Microsoft Excel 365

Standards and calibration information: /

Experimental conditions: Laser power, laser modality, treatment time, type of bacterial biofilm, PDMS stiffness, model system geometry

--------------------------------------------------DATA-SPECIFIC INFORMATION: [wedge-shaped model cleaning.xlsx]--------------------------------------------------Each sheet contains the observation position on the sample and the corresponding percentage of cleaned surface.

Sheet 1: Measurements at 10% PDMS with different energy settings of the USP laser modalitySheet 2: Measurements at 4% PDMS with different energy settings of the USP laser modalitySheet 3: Measurements using AutoSWEEPS laser modality at 20 mJ with different PDMS valuesSheet 4: Measurements at 10% PDMS with different laser tip positions using USP modalitySheet 5: Measurements using a hydrodynamic pump at different PDMS valuesSheet 6: Measurements at 4% PDMS with different treatment durations using USP modalitySheet 7: Measurements at 10% PDMS with removal of different bacterial biofilm types using USP modality

Variables: Position, replicates, mean (%), standard error

--------------------------------------------------DATA-SPECIFIC INFORMATION: [narrow-gap model cleaning.xlsx]--------------------------------------------------Each sheet contains the observation position on the sample and the corresponding percentage of cleaned surface.Measurement conditions (laser modality and laser tip position) are specified above each table.

Variables: Position, replicates, mean (%), standard error