Biofilms are surface-attached microbial communities whose architecture can be captured with confocal microscopy. Manual or automatic thresholding of acquired images is often needed to help distinguish biofilm biomass from background noise. However, manual thresholding is subjective and current automatic thresholding methods can lead to loss of meaningful data. Here, we describe an automatic thresholding method designed for confocal fluorescent signal, termed the biovolume elasticity method (BEM). We evaluated BEM using confocal image stacks of oral biofilms grown in pooled human saliva. Image stacks were thresholded manually and automatically with three different methods; Otsu, iterative selection (IS), and BEM. Effects on biovolume, surface area, and number of objects detected indicated that the BEM was the least aggressive at removing signal, and provided the greatest visual and quantitative acuity of single cells. Thus, thresholding with BEM offers a sensitive, automatic, and tunable method to maintain biofilm architectural properties for subsequent analysis.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115396 | PMC |
| http://dx.doi.org/10.1038/s41598-018-31012-5 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Integration of Motion and Stillness: A Paradigm Shift in Constructing Nearly Planar NIR-II AIEgen with Ultrahigh Molar Absorptivity and Photothermal Effect for Multimodal Phototheranostics.
J Am Chem Soc
January 2025
Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, and Department of Chemical & Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China.
The two contradictory entities in nature often follow the principle of unity of opposites, leading to optimal overall performance. Particularly, aggregation-induced emission luminogens (AIEgens) with donor-acceptor (D-A) structures exhibit tunable optical properties and versatile functionalities, offering significant potential to revolutionize cancer treatment. However, trapped by low molar absorptivity (ε) owing to the distorted configurations, the ceilings of their photon-harvesting capability and the corresponding phototheranostic performance still fall short.
View Article and Find Full Text PDFSupramolecular Gelation Based on Native Amino Acid Tyrosine and Its Charge-Transfer Complex Formation.
Langmuir
January 2025
Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
Self-assembly of amino acids and short-peptide derivatives attracted significant curiosity worldwide due to their unique self-assembly process and wide variety of applications. Amino acid is considered one of the important synthons in supramolecular chemistry. Self-assembly processes and applications of unfunctionalized native amino acids have been less reported in the literature.
View Article and Find Full Text PDFCT Multidimensional Radiomics Combined with Inflammatory Immune Score For Preoperative Prediction of Pathological Grade in Esophageal Squamous Cell Carcinoma.
Acad Radiol
January 2025
Department of Radiology, Luzhou People's Hospital, Luzhou 646000, China (S.Z., J.C., A.R., X.Z., J.H., M.Y., F.W.). Electronic address:
Rationale And Objectives: Inflammation and immune biomarkers can promote angiogenesis and proliferation and metastasis of esophageal squamous cell carcinoma (ESCC). The degree of pathological grade reflects the tumor heterogeneity of ESCC. The purpose is to develop and validate a nomogram based on enhanced CT multidimensional radiomics combined with inflammatory immune score (IIS) for predicting poorly differentiated ESCC.
View Article and Find Full Text PDFGrids designed for tomography: Stereovision transmission electron microscopy makes it easy to determine the winding handedness of helical nanocoils.
Micron
January 2025
Health and Medical Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central-6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. Electronic address:
Determining the handedness of helical nanocoils using transmission electron microscopy (TEM) has traditionally been challenging due to the deep depth of field and transmission nature of TEM, complementary techniques are considered necessary and have been practiced such as low angle rotary shadowing, scanning electron microscopy (SEM), or atomic force microscopy (AFM). These methods require customized sample preparation, making direct comparison difficult. Inspired by the need to identify the helical winding direction from TEM images alone, we developed a specialized tomography grid to capture stereo-pair images, enabling stereopsis.
View Article and Find Full Text PDFEstablishing a Three-Dimensional Coculture Module of Epithelial Cells Using Nanofibrous Membranes.
J Vis Exp
December 2024
Department of Pharmacology, School of Medicine, Ajou University; 3D Immune System Imaging Core Center, Ajou University;
Technical hurdles in a culture of epithelial cells include dedifferentiation and loss of function. Biomimetic three-dimensional (3D) cell culture methods can enhance cell culture efficiency. This study introduces an advanced two-layered culture system intended to cultivate epithelial cells as tissue-like layers with the culture of fibroblasts within a 3D environment.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!