spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos

Thiels, Wim; Smeets, Bart; Cuvelier, Maxim; Caroti, Francesca; Jelier, Rob

doi:10.1093/bioinformatics/btab557

Cited by 14 publications

(28 citation statements)

References 33 publications

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“…The motivation is that high overall cortical tension makes cells more rigid and spherical, similar to when cells round up prior to mitosis by increasing cortical stiffness and tension (Stewart et al, 2011), whereas lower cortical tension allows more flexible and irregular shapes. We employed a novel cellular segmentation pipeline to retrieve the shapes of the cells from confocal microscopy images of embryos with fluorescently membranes (strain RJ013) (Thiels et al, 2021). Over time, E retains a mostly spherical shape, whereas MS develops a more irregular shape, and in some embryos forms a lamellipodium structure 4.5 min after EMS division (Figure 2E, MS lamellipodium in embryos 1 and 2, see Supplementary Figure 1 for sphericity measures).…”

Section: Resultsmentioning

confidence: 99%

“…When comparing volume and sphericity over time (Figure 3, Supplementary Figures 1, 2), mixed effect models were fitted with lmer, with random effects capturing embryo specific effects and evaluating temporal correlations. Volume ratios were modeled as described in the paper describing the segmentation methodology (Thiels et al, 2021). The model for sphericity of the E-cell using the lmer-package syntax is expressed as:…”

Section: Statistical Analyses and Visualizationmentioning

confidence: 99%

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Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell

Caroti

Thiels

Vanslambrouck

et al. 2021

Front. Cell Dev. Biol.

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During asymmetrical division of the endomesodermal precursor cell EMS, a cortical flow arises, and the daughter cells, endodermal precursor E and mesodermal precursor MS, have an enduring difference in the levels of F-actin and non-muscular myosin. Ablation of the cell cortex suggests that these observed differences lead to differences in cortical tension. The higher F-actin and myosin levels in the MS daughter coincide with cell shape changes and relatively lower tension, indicating a soft, actively moving cell, whereas the lower signal in the E daughter cell is associated with higher tension and a more rigid, spherical shape. The cortical flow is under control of the Wnt signaling pathway. Perturbing the pathway removes the asymmetry arising during EMS division and induces subtle defects in the cellular movements at the eight-cell stage. The perturbed cellular movement appears to be associated with an asymmetric distribution of E-cadherin across the EMS cytokinesis groove. ABpl forms a lamellipodium which preferentially adheres to MS by the E-cadherin HMR-1. The HMR-1 asymmetry across the groove is complete just at the moment cytokinesis completes. Perturbing Wnt signaling equalizes the HMR-1 distribution across the lamellipodium. We conclude that Wnt signaling induces a cortical flow during EMS division, which results in a transition in the cortical contractile network for the daughter cells, as well as an asymmetric distribution of E-cadherin.

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Section: Resultsmentioning

confidence: 99%

Section: Statistical Analyses and Visualizationmentioning

confidence: 99%

Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell

Caroti

Thiels

Vanslambrouck

et al. 2021

Front. Cell Dev. Biol.

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“…Embryo compression occurs naturally in-utero , while in-vitro it generally occurs as a result of sample preparation for imaging, where the degree of compression depends on the mounting technique used [14]. The initial geometry of the compressed embryo was based on segmented egg shapes obtained from microscopy data [15], while the uncompressed shape was estimated by fitting an ellipsoid with the same volume [41]. The spindle offset α for each cell division was statistically sampled from experimental data in compressed conditions from Fickentscher and Weiss [6].…”

Section: Resultsmentioning

confidence: 99%

“…This supports the notion that position α and angle φ of the mitotic spindle are highly robust predictors for volume asymmetry in the C. elegans cleavage phase. We hypothesized that the effect of confinement alone is sufficient to explain the different volume ratio observed in experiments [15]. To this end, we adopted spindle positions from experiments in confined conditions, but simulated development in an uncompressed egg geometry.…”

Section: Spindle Positioning During Early C Elegans Developmentmentioning

confidence: 99%

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Stability of asymmetric cell division under confinement: A deformable cell model of cytokinesis applied to C. elegans development

Cuvelier

Thiels

Jelier

et al. 2022

Preprint

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Cell division during early embryogenesis has been linked to key morphogenic events such as embryo symmetry breaking and tissue patterning. It is thought that boundary conditions together with cell intrinsic cues act as a mechanical “mold”, guiding cell division to ensure these events are more robust. We present a novel computational mechanical model of cytokinesis, the final phase of cell division, to investigate how cell division is affected by mechanical and geometrical boundary conditions. The model reproduces experimentally observed furrow dynamics and predicts the volume ratio of daughter cells in asymmetric cell divisions based on the position and orientation of the mitotic spindle. We show that the orientation of confinement relative to the division axis modulates the volume ratio in asymmetric cell division and quantified the mechanical contribution of cortex mechanics, relative to the mechanical properties of the furrow ring. We apply this model to early C. elegans development, which proceeds within the confines of an eggshell, and simulate the formation of the three body axes via sequential (a)symmetric divisions up until the six cell stage. We demonstrate that spindle position and orientation alone can be used to predict the volume ratio of daughter cells during the cleavage phase of development. However, for compression perturbed egg geometries, the model predicts that the change in confinement alone is insufficient to explain experimentally observed differences in cell volume, inferring an unmodeled underlying spindle positioning mechanism. Finally, the model predicts that confinement stabilizes asymmetric cell divisions against bubble-instabilities, which can arise due to elevated mitotic cortical tension.

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CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo

Cao,

Hu,

Guan

et al. 2024

Quant. Biol.

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Caenorhabditis elegans has been widely used as a model organism in developmental biology due to its invariant development. In this study, we developed a desktop software CShaperApp to segment fluorescence‐labeled images of cell membranes and analyze cellular morphologies interactively during C. elegans embryogenesis. Based on the previously proposed framework CShaper, CShaperApp empowers biologists to automatically and efficiently extract quantitative cellular morphological data with either an existing deep learning model or a fine‐tuned one adapted to their in‐house dataset. Experimental results show that it takes about 30 min to process a three‐dimensional time‐lapse (4D) dataset, which consists of 150 image stacks at a ∼1.5‐min interval and covers C. elegans embryogenesis from the 4‐cell to 350‐cell stages. The robustness of CShaperApp is also validated with the datasets from different laboratories. Furthermore, modularized implementation increases the flexibility in multi‐task applications and promotes its flexibility for future enhancements. As cell morphology over development has emerged as a focus of interest in developmental biology, CShaperApp is anticipated to pave the way for those studies by accelerating the high‐throughput generation of systems‐level quantitative data collection. The software can be freely downloaded from the website of Github (cao13jf/CShaperApp) and is executable on Windows, macOS, and Linux operating systems.

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spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos

Cited by 14 publications

References 33 publications

Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell

Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell

Stability of asymmetric cell division under confinement: A deformable cell model of cytokinesis applied to C. elegans development

CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo

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