MAARS: a novel high-content acquisition software for the analysis of mitotic defects in fission yeast

Li, Tong; Mary, Hadrien; Grosjean, Marie; Fouchard, Jonathan; Cabello-Aguilar, Simon; Reyes, Céline; Tournier, Sylvie; Gachet, Yannick

doi:10.1091/mbc.e16-10-0723

Cited by 14 publications

(16 citation statements)

References 64 publications

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“…This allows users to run any pipeline of their choice for 2D cell segmentation (e.g. 33,34,41 ) while still profiting from Pomegranate's 3D reconstruction. We demonstrate this by using 2D brightfield segmentation obtained by "YeaZ" 41 , a convolutional neural network (CNN) trained on yeast brightfield images ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…To obtain the midplane ROI, the characteristic intensity pattern surrounding cells in the brightfield image (Supplementary Fig. S3 ) is used to define the edges of the cell 33 , 35 , 40 (Fig. 1 B, see “ Materials and methods ” for details).…”

Section: Resultsmentioning

confidence: 99%

“…Adapted from the MAARs pipeline 33 , an optional solidity filter was used to exclude some ROIs that do not represent cells. An ROI's solidity is the ratio of its area and its convex hull area, where a value of 1 indicates a completely convex object.…”

Section: Methodsmentioning

confidence: 99%

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Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

Baybay

Esposito

Hauf

2020

Sci Rep

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Three-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regions. The diameter of these spheres adapts to the cell diameter at each position. Thus, Pomegranate accurately represents radially symmetric cells in 3D even if cell diameter varies and regardless of whether a cell is straight, bent or curved. We have tested Pomegranate on fission yeast and demonstrate its ability to 3D segment wild-type cells as well as classical size and shape mutants. The pipeline is available as a macro for the open-source image analysis software Fiji/ImageJ. 2D segmentations created within or outside Pomegranate can serve as input, thus making this a valuable extension to the image analysis portfolio already available for fission yeast and other radially symmetric cell types.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

Baybay

Esposito

Hauf

2020

Sci Rep

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“…For image segmentation, the AutoCalibrationCurve macro used the Mitotic Analysis and Recording System (MAARS) ( Li et al, 2017 ) plugin for ImageJ. The MAARS plugin automatically circled cells in sum projections of fluorescence images using 21 bright-field Z-sections spaced 0.6 μm apart ( Fig S4A ).…”

Section: Methodsmentioning

confidence: 99%

Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

2018

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“…Cells in sum projection images were automatically circled using the Mitotic Analysis and Recording System (MAARS) (Li et al, 2017) plugin for ImageJ using 21 bright-field Z-sections spaced 0.6 µm apart (Fig. S3 B).…”

Section: Generating the Calibration Curve And Calculating Number Of Mmentioning

confidence: 99%

Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

Epstein

Espinoza-Sanchez

Pollard

2018

Preprint

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Previous research concluded that phosphorylation at three sites on Arp2 is necessary to activate Arp2/3 complex. Epstein et al. make genomic substitutions blocking or mimicking phosphorylation to demonstrate that phosphorylation of these three sites does not regulate Arp2/3 complex in fission yeast. AbstractLeClaire et al. presented evidence that phosphorylation of three sites on the Arp2 subunit activates Arp2/3 complex to nucleate actin filaments. We mutated the homologous residues of Arp2 (Y198, T233 and T234) in the fission yeast genome to amino acids that preclude or mimic phosphorylation. Arp2/3 complex is essential for the viability of fission yeast, yet strains unable to phosphorylate these sites grew normally. Y198F/T233A/T234A Arp2 was only nonfunctional if GFP-tagged, as observed by LeClaire et al. in Drosophila cells. Replacing both T233 and T234 with aspartic acid was lethal, suggesting that phosphorylation might be inhibitory.Nevertheless, blocking phosphorylation at these sites had the same effect as mimicking it: slowing assembly of endocytic actin patches. Mass spectrometry revealed phosphorylation at a fourth conserved Arp2 residue, Y218, but both blocking and mimicking phosphorylation of Y218 only slowed actin patch assembly slightly. Therefore, phosphorylation of Y198, T233, T234 and Y218 is not required for the activity of fission yeast Arp2/3 complex.

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MAARS: a novel high-content acquisition software for the analysis of mitotic defects in fission yeast

Cited by 14 publications

References 64 publications

Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

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