scholarly journals A methodology for morphological feature extraction and unsupervised cell classification

2019 ◽  
Author(s):  
Dhananjay Bhaskar ◽  
Darrick Lee ◽  
Hildur Knútsdóttir ◽  
Cindy Tan ◽  
MoHan Zhang ◽  
...  
Keyword(s):  
Cell Shape ◽  
Biological Data ◽  
Computer Assisted ◽  
Shape Classification ◽  
Cell Classification ◽  
Important Indicator ◽  
Microscopic Images ◽  
Density Based Clustering ◽  
Cell Shapes ◽  
Microscopy Images

AbstractCell morphology is an important indicator of cell state, function, stage of development, and fate in both normal and pathological conditions. Cell shape is among key indicators used by pathologists to identify abnormalities or malignancies. With rapid advancements in the speed and amount of biological data acquisition, including images and movies of cells, computer-assisted identification and analysis of images becomes essential. Here, we report on techniques for recognition of cells in microscopic images and automated cell shape classification. We illustrate how our unsupervised machine-learning-based approach can be used to classify distinct cell shapes from a large number of microscopic images.Technical AbstractWe develop a methodology to segment cells from microscopy images and compute quantitative descriptors that characterize their morphology. Using unsupervised techniques for dimensionality reduction and density-based clustering, we perform label-free cell shape classification. Cells are identified with minimal user input using mathematical morphology and region-growing segmentation methods. Physical quantities describing cell shape and size (including area, perimeter, Feret diameters, etc.) are computed along with other features including shape factors and Hu’s image moments.Correlated features are combined to obtain a low-dimensional (2-D or 3-D) embedding of data points corresponding to individual segmented cell shapes. Finally, a hierarchical density-based clustering algorithm (HDBSCAN) is used to classify cells. We compare cell classification results obtained from different combinations of features to identify a feature set that delivers optimum classification performance for our test data consisting of phase-contrast microscopy images of a pancreatic-cancer cell line, MIA PaCa-2.

scholarly journals Cell-based Simulations of Biased Epithelial Lung Growth

2019 ◽  
Author(s):  
Anna Stopka ◽  
Marco Kokic ◽  
Dagmar Iber
Keyword(s):  
Cell Division ◽  
Cell Shape ◽  
Longitudinal Direction ◽  
Simulation Software ◽  
Biological Data ◽  
Surrounding Tissue ◽  
Cortical Tension ◽  
Lung Epithelial ◽  
Cell Shapes ◽  
Mammalian Lung

AbstractDuring morphogenesis, epithelial tubes elongate. In case of the mammalian lung, biased elongation has been linked to a bias in cell shape and cell division, but it has remained unclear whether a bias in cell shape along the axis of outgrowth is sufficient for biased outgrowth and how it arises. Here, we use our 2D cell-based tissue simulation software LBIBCell to investigate the conditions for biased epithelial outgrowth. We show that the observed bias in cell shape and cell division can result in the observed bias in outgrowth only in case of strong cortical tension, and comparison to biological data suggests that the cortical tension in epithelia is likely sufficient. We explore mechanisms that may result in the observed bias in cell division and cell shapes. To this end, we test the possibility that the surrounding tissue or extracellular matrix acts as a mechanical constraint that biases growth in longitudinal direction. While external compressive forces can result in the observed bias in outgrowth, we find that they do not result in the observed bias in cell shapes. We conclude that other mechanisms must exist that generate the bias in lung epithelial outgrowth.

Development of software and modification of Q-FISH protocol for estimation of individual telomere length in immunopathology

2017 ◽  
Vol 15 (02) ◽  
pp. 1650041 ◽  
Author(s):  
M. Sh. Barkovskaya ◽  
A. G. Bogomolov ◽  
N. Yu. Knauer ◽  
N. B. Rubtsov ◽  
V. A. Kozlov
Keyword(s):  
Telomere Length ◽  
Inflammatory Diseases ◽  
Quantitative Information ◽  
Computer Assisted ◽  
Metaphase Chromosomes ◽  
Important Indicator ◽  
Background Fluorescence ◽  
Immune Mediated ◽  
Light Effects ◽  
Assisted Analysis

Telomere length is an important indicator of proliferative cell history and potential. Decreasing telomere length in the cells of an immune system can indicate immune aging in immune-mediated and chronic inflammatory diseases. Quantitative fluorescent in situ hybridization (Q-FISH) of a labeled (C3TA[Formula: see text] peptide nucleic acid probe onto fixed metaphase cells followed by digital image microscopy allows the evaluation of telomere length in the arms of individual chromosomes. Computer-assisted analysis of microscopic images can provide quantitative information on the number of telomeric repeats in individual telomeres. We developed new software to estimate telomere length. The MeTeLen software contains new options that can be used to solve some Q-FISH and microscopy problems, including correction of irregular light effects and elimination of background fluorescence. The identification and description of chromosomes and chromosome regions are essential to the Q-FISH technique. To improve the quality of cytogenetic analysis after Q-FISH, we optimized the temperature and time of DNA-denaturation to get better DAPI-banding of metaphase chromosomes. MeTeLen was tested by comparing telomere length estimations for sister chromatids, background fluorescence estimations, and correction of nonuniform light effects. The application of the developed software for analysis of telomere length in patients with rheumatoid arthritis was demonstrated.

scholarly journals Automated Three-Dimensional Detection and Shape Classification of Dendritic Spines from Fluorescence Microscopy Images

PLoS ONE ◽  
2008 ◽  
Vol 3 (4) ◽  
pp. e1997 ◽  
Author(s):  
Alfredo Rodriguez ◽  
Douglas B. Ehlenberger ◽  
Dara L. Dickstein ◽  
Patrick R. Hof ◽  
Susan L. Wearne
Keyword(s):  
Fluorescence Microscopy ◽  
Dendritic Spines ◽  
Three Dimensional ◽  
Shape Classification ◽  
Microscopy Images

Computer-assisted long-term measurements of urinary output and other biological data

1990 ◽  
Vol 258 (1) ◽  
pp. R274-R280 ◽  
Author(s):  
H. W. Reinhardt ◽  
U. Palm ◽  
R. Mohnhaupt ◽  
K. Dannenberg ◽  
W. Boemke
Keyword(s):  
Sodium Excretion ◽  
Biological Data ◽  
Computer Assisted ◽  
Indwelling Catheters ◽  
Integrative Physiology ◽  
Short Intervals ◽  
Physiological Variables ◽  
Cyclic Variations ◽  
Computerized System

A computerized system is described, combining automatic collection of urine in short intervals (minutes) over long periods (days) and recordings of body temperature, MABP, and heart rate in chronically instrumented conscious dogs. During the studies the dogs are housed in metabolic cages. Indwelling catheters and electrical wires are connected to a specially designed swivel and directed out of the cage to the next room. Infusions, blood sampling, and monitoring can be performed from this room without disturbance to the dogs. Three examples of recordings are given. In one of these examples the sodium excretion patterns on 5 consecutive days under continuous saline infusion in one dog is evaluated. Urine was collected every 20 min. Sodium excretion showed cyclic variations. Fourier analysis exhibited 18-h periods and 4- to 8-h periods. The described system renders, e.g., coherent time series analysis possible for a variety of simultaneously recorded physiological variables and may thus acquire considerable importance for integrative physiology.

Regulation of cell shape in Euglena gracilis. III. Involvement of stable microtubules

1985 ◽  
Vol 74 (1) ◽  
pp. 219-237
Author(s):  
C.L. Lachney ◽  
T.A. Lonergan
Keyword(s):  
Euglena Gracilis ◽  
Cell Shape ◽  
Microtubule Assembly ◽  
Live Cells ◽  
Microtubule Depolymerization ◽  
Cytoplasmic Microtubule ◽  
Intact Cells ◽  
Calmodulin Antagonist ◽  
Cell Shapes ◽  
In Cells

The role of cytoplasmic microtubules in a recently reported biological clock-controlled rhythm in cell shape of the alga Euglena gracilis (strain Z) was examined using indirect immunofluorescence microscopy. The resulting fluorescent patterns indicated that, unlike many other cell systems, Euglena cells apparently change from round to long to round cell shape without associated cytoplasmic microtubule assembly and disassembly. Instead, the different cell shapes were correlated with microtubule patterns, which suggested that movement of stable microtubules to accomplish cell shape changes. In live intact cells, these microtubules were demonstrated by immunofluorescence to be stable to lowered temperature and elevated intracellular Ca2+ levels, treatments that are commonly used to depolymerize microtubules. In cells extracted in detergent at low temperature or in the presence of elevated Ca2+ levels, the fluorescent image of the microtubules was disrupted. Transmission electron microscopy confirmed the loss of one subset of pellicle microtubules. The difference in microtubule stability to these agents between live intact cells and cells extracted in detergent suggested the presence of a microtubule-stabilizing factor in live cells, which is released from the cell by extraction with detergent, thereby permitting microtubule depolymerization by Ca2+ or lowered temperature. The calmodulin antagonist trifluoperazine prevented the Ca2+-induced disruption of the fluorescent microtubule pattern in cells extracted in detergent. These results implied the involvement of calmodulin in the sensitivity to Ca2+ of the microtubules of cells extracted in detergent.

scholarly journals Molar Bud-to-Cap Transition Is Proliferation Independent

2019 ◽  
Vol 98 (11) ◽  
pp. 1253-1261 ◽  
Author(s):  
S. Yamada ◽  
R. Lav ◽  
J. Li ◽  
A.S. Tucker ◽  
J.B.A. Green
Keyword(s):  
Cell Proliferation ◽  
Cell Shape ◽  
Tooth Germ ◽  
Odontogenic Epithelium ◽  
Differential Cell ◽  
Cell Shapes ◽  
Genetic Mechanisms ◽  
Cell Trajectory ◽  
Tooth Germs ◽  
Different Parts

Tooth germs undergo a series of dynamic morphologic changes through bud, cap, and bell stages, in which odontogenic epithelium continuously extends into the underlying mesenchyme. During the transition from the bud stage to the cap stage, the base of the bud flattens and then bends into a cap shape whose edges are referred to as “cervical loops.” Although genetic mechanisms for cap formation have been well described, little is understood about the morphogenetic mechanisms. Computer modeling and cell trajectory tracking have suggested that the epithelial bending is driven purely by differential cell proliferation and adhesion in different parts of the tooth germ. Here, we show that, unexpectedly, inhibition of cell proliferation did not prevent bud-to-cap morphogenesis. We quantified cell shapes and actin and myosin distributions in different parts of the tooth epithelium at the critical stages and found that these are consistent with basal relaxation in the forming cervical loops and basal constriction around enamel knot at the center of the cap. Inhibition of focal adhesion kinase, which is required for basal constriction in other systems, arrested the molar explant morphogenesis at the bud stage. Together, these results show that the bud-to-cap transition is largely proliferation independent, and we propose that it is driven by classic actomyosin-driven cell shape–dependent mechanisms. We discuss how these results can be reconciled with the previous models and data.

scholarly journals An effective model for quantification of cell 3Dshape in early embryogenesis

2021 ◽  
Author(s):  
Zelin Li ◽  
Jianfeng Cao ◽  
Zhongying Zhao ◽  
Hong Yan
Keyword(s):  
Cell Fate ◽  
Cell Shape ◽  
Developmental Process ◽  
Morphological Changes ◽  
Shape Space ◽  
Effective Model ◽  
Cell Stage ◽  
Cell Shapes ◽  
Dimensional Shape ◽  
Low Dimensional

Abstract Background: The developmental process is featured by fabulous morphogenesis in multicellular organisms. Describing morphological changes quantitatively concretes the way to investigating both intra and inter cell regulations on cell fate. While Caenorhabditis elegans has been used as a model for cell and development studies for a long time, the exploration of how cell shape is precisely controlled keeps obscured by the lack of methods to model morphological features. Currently, in order to characterize the features of cell shape involved in cell migration and differentiation, there is an increasing demand in analyzing cell shape systematically, especially when many works have contributed to cell reconstruction. Results: In this work, Spherical harmonics and Principal component analysis integrated Cell Shape quantification Models (SPCSMs) is proposed to represent cell shapes in a low-dimensional shape space. SPCSMs incorporates a complete pipeline to quantify cell shapes and analyze their morphological phenotypes in three dimensional (3D) reconstructions. Based on the framework, we extract biological patterns in the lineage of C. elegans embryo before 350-cell stage, during which all hypodermis cells deformed like a funnel and can be recognized by this shape pattern. Finally, SPCSMs is compared with two cell shape representation methods, which substantiates the effectiveness and robustness of our method. Conclusion: SPCSMs provides a general method to decribe shapes in low-dimensional shape space with compact parameters. It can quantify the shapes of cells from single-cell resolution images obtained over one-minute intervals, making it possible for the recognition of developmental patterns in cell lineages. SPCSMs is expected to be an effective model for biologists to explore the relationships between the shapes of cells and their fates.

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