Different binarization processes validated against manual counts of fluorescent bacterial cells

Tamminga, Gerrit G.; Paulitsch-Fuchs, Astrid H.; Jansen, Gijsbert J.; Euverink, Gert-Jan

doi:10.1016/j.mimet.2016.07.003

Cited by 5 publications

(5 citation statements)

References 23 publications

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“…In addition, all methods displayed strong agreement, presenting similar results. It was observed that there is no difference in the significance between the three types of analysis, and similar results to this study were demonstrated in the literature using different experimental conditions (Reyes‐Fernandez et al, 2019; Tamminga et al, 2016), confirming that the automated and semi‐automated method proposed can be used reliably.…”

Section: Discussionsupporting

confidence: 90%

“…The limitations of the proposed automated method should be discussed. The global threshold for all images and the process of segmentation produce some issues, such as the loss of information (Kim et al, 2018; Reyes‐Fernandez et al, 2019; Tamminga et al, 2016). Therefore, it is necessary to conduct more studies on automatization applications in microscopic analysis for the improvement of segmentation tools.…”

Section: Discussionmentioning

confidence: 99%

Section: Limitationsmentioning

confidence: 99%

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Automated bone healing evaluation: New approach to histomorphometric analysis

Linhares

Rabelo

Limirio

et al. 2022

Microscopy Res & Technique

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This study aimed to assess different approaches for bone healing evaluation on histological images and to introduce a new automatic evaluation method based on segmentation with distinct thresholds. We evaluated the hyperbaric oxygen therapy (HBO) effects on bone repair in type 1 diabetes mellitus rats. Twelve animals were divided into four groups (n = 3): non‐diabetic, non‐diabetic + HBO, diabetic, and diabetic + HBO. Diabetes was induced by intravenous administration of streptozotocin (50 mg/kg). Bone defects were created in femurs and HBO was immediately started at one session/day. After 7 days, the animals were euthanized, femurs were removed, demineralized, and embedded in paraffin. Histological sections were stained with hematoxylin and eosin (HE) and Mallory's trichrome (MT), and evaluated using three approaches: (1) conventional histomorphometric analysis (HE images) using a 144‐point grid to quantify the bone matrix; (2) a semi‐automatic method based on bone matrix segmentation to assess the bone matrix percentage (MT images); and (3) automatic approach, with the creation of a plug‐in for ImageJ software. The time required to perform the analysis in each method was measured and subjected to Bland–Altman statistical analysis. All three methods were satisfactory for measuring bone formation and were not statistically different. The automatic approach reduced the working time compared to visual grid and semi‐automated method (p < .01). Although histological evaluation of bone healing was performed successfully using all three methods, the novel automatic approach significantly shortened the time required for analysis and had high accuracy.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

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Automated bone healing evaluation: New approach to histomorphometric analysis

Linhares

Rabelo

Limirio

et al. 2022

Microscopy Res & Technique

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“…This method of cell density detection requires cells to be uniformly distributed in the liquid, and then to count the cells in certain volume of sample [11][12][13][14] . Commonly used methods for detecting cells are laser induced uorescence method [15][16][17][18][19] , image processing method [20][21][22][23][24][25][26] and electrical impedance method [27][28][29][30] . Ivan V Grishagin designed a cell counting program based on image processing, which obtains images of mammalian cell suspension in the hemocytometer component through a conventional optical microscope equipped with a network camera [31] .…”

Section: Introductionmentioning

confidence: 99%

Cell density detection based on a microfluidic chip with two electrode pairs

2022

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Cell density detection is usually the counting of cells in certain volume of liquid, which is an important process in the eld of biomedicine. The Coulter counting method has been an important method for biological cell detection and counting for decades. In this paper, a micro uidic chip based on two electrode pairs is designed, which uses the Coulter principle to detect the ow rate of uncertain volume liquid and count the cells, and then calculate the cell density by statistics. When the cell passes through the sensor channel formed by the electrode pair on the chip, the impedance will change between the electrodes. This phenomenon has been proved by experiments. The designed chip has the advantages of simple structure, small size and low manufacturing cost. The cell density detection method proposed in this article is of great signi cance to the research in the eld of biological cell detection and development of related medical devices.

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“…The samples can either be directly analysed or in combination with staining methods for the detection of specific biomolecules or structures inside the cell. Examples of these well-known methods are Fluorescence In Situ Hybridisation (FISH) or direct staining of DNA/ RNA using fluorescent labels like propidium iodide, acridine orange, Cyanine 3, or, Fluorescein isothiocyanate (Hoshino et al, 2008;Langendijk et al, 1995;Poulsen et al, 1993;Seo et al, 2010;Tamminga et al, 2016;Waters and Swedlow, 2007).…”

Section: Introductionmentioning

confidence: 99%

Development and validation of an alternative parameter for quantification of signals emitted by fluorescently labelled bacteria in microscopic images

Tamminga¹,

Paulitsch-Fuchs

Jansen³

et al. 2019

Journal of Microbiological Methods

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In this study, an alternative parameter for quantifying the signals of fluorescently labelled bacteria (e.g. propidium iodide, Cyanine 3, etc.) in microscopic images was investigated. Three common parameters (mean grey value (MGV), mean grey value which is corrected for the background (MGVcwB) and the signal to background ratio (SBR) per bacterial cell) are used as reference parameters. As an alternative, the coefficient of variation (CV) is defined as the ratio of the logarithm of the standard deviation and the logarithm of the mean grey value of a bacterial cell in a microscopic image. The actual fluorescence value was safeguarded by measuring commercially available fluorescence latex microspheres at regular time intervals within our study. The precision and the correlation of the respective values of MGV, MGVcwB, SBR and CV taken from identical images were measured and subsequently normalized in order to enhance the inter-parameter comparability. The average precision of CV was the highest (89% ± 14) with decreasing numbers for MGVcwB, SBR, and MGV (78% ± 25, 71% ± 32, and, 52% ± 22, respectively). Changes in operational parameters, e.g., microscope settings, protocol steps, etc., yielded good results for the CV but less precise results for MGV, MGVcwB, and SBR in the analyses of identical images.In conclusion, using the alternative parameter CV, changes in the composition of microbial ecosystems may thus be investigated at the highest precision level.

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Different binarization processes validated against manual counts of fluorescent bacterial cells

Cited by 5 publications

References 23 publications

Automated bone healing evaluation: New approach to histomorphometric analysis

Automated bone healing evaluation: New approach to histomorphometric analysis

Cell density detection based on a microfluidic chip with two electrode pairs

Development and validation of an alternative parameter for quantification of signals emitted by fluorescently labelled bacteria in microscopic images

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