Metadata management for high content screening in OMERO

Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Gus; Flynn, Helen; Gillen, Kenneth; Leigh, R. A.; Lindner, Dominik; Linkert, Melissa; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Allan, Chris; Burel, Jean Marie; Moore, Josh; Swedlow, Jason R.

doi:10.1016/j.ymeth.2015.10.006

Cited by 41 publications

(35 citation statements)

References 34 publications

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“…To image embryos at the cortex, we typically moved the focus to 12 to 15 µm below the spindle plane. Images were then stored using Omero software (Li et al, 2016).…”

Section: Imaging Of Microtubule Contacts At the Cortexmentioning

confidence: 99%

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The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex

Bouvrais

Chesneau

Cunff

et al. 2019

Preprint

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In the Caenorhabditis elegans zygote, astral microtubules generate forces, pushing against and pulling from the cell periphery. They are essential to position the mitotic spindle and in turn the cytokinesis furrow, ensuring the proper distribution of fate determinants to the daughter cells. By measuring the dynamics of astral microtubules, we revealed the presence of two populations, residing at the cortex during 0.4 s and 1.8 s, proposed to reflect the pulling and pushing events, respectively. This is a unique opportunity to unravel the time and space variations of these both spindle-positioning forces, to study their regulation under physiological conditions. By an investigation at the microscopic level, we first confirmed that the asymmetry in pulling forces was encoded by an anteroposterior imbalance in dynein-engaging rate, and that this asymmetry exists from early metaphase on and accounts for the final spindle position. More importantly, we obtained direct proof of the temporal control of pulling forces through the forcegenerator processivity increase during anaphase. Lastly, we discovered an anti-correlation between the long-lived population density and the stability of the spindle position during metaphase, which strongly suggests that the pushing forces contribute to maintaining the spindle at the cell centre.

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“…To image embryos at the cortex, we typically moved the focus to 12 to 15 µm below the spindle plane. Images were then stored using Omero software (Li et al, 2016).…”

Section: Imaging Of Microtubule Contacts At the Cortexmentioning

confidence: 99%

“…Images were acquired with an Andor iXon3 EMCCD 512x512 camera at 33 frames per second and using their Solis software. Images were then stored using Omero software (Li et al, 2016).…”

Section: Spindle Pole Imagingmentioning

confidence: 99%

The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex

Bouvrais

Chesneau

Cunff

et al. 2019

Preprint

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“…Images were acquired with an Andor iXon3 EMCCD 512x512 camera at 33 frames per second and using their Solis software. Images were then stored using omero software (32). Except if histones were labelled (Table 1), the beginning of the spindle's abrupt elongation ( Figure S4) was used as the marker for anaphase onset (33), and the centrosome tracks of individual embryos were aligned using this reference, for averaging purposes or for overlay on the "landing" assay.…”

Section: Centrosome Imagingmentioning

confidence: 99%

LET-99-dependent spatial restriction of active force generators makes spindle’s position robust

Bouvrais¹,

Chesneau²,

Pastezeur³

et al. 2017

Preprint

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Background: During asymmetric division of the Caenorhabditis elegans nematode zygote, the polarity cues distribution and daughter cell fates depend on the correct positioning of the mitotic spindle which results from both centering and cortical pulling forces. Revealed by spindle rocking, these pulling forces are regulated by the force generator dynamics, which are related to mitosis progression. This may be combined with a second regulation, this one by the posterior spindle pole position, which can be seen when comparing related species. Results: After delaying anaphase onset, we identified a positional pulling force regulation in C. elegans, which we ascribed to microtubule dynamics at the cortex. Indeed, in mapping the contacts we found a correlation between the centrosome-cortex distance and the microtubule contact density. This density in turn modulates pulling force generator activity. We expanded our model of spindle rocking and predicted then experimentally validated that the oscillation onset position resists changes in cellular geometry and number of force generators. Consistent with final spindle position measurements, this new model accounts for a lower dependence on force generator dynamics and quantities than predicted by the previous model. Conclusion: The spindle position regulates the rapid increase in forces needed for anaphase oscillation and positioning through the spatial modulation of microtubule-cortex contacts. This regulation superimposes that of force generator processivity, putatively linked to the cell cycle. This novel control confers resistance to variations in zygote geometry and dynamics of cortical force generators. Interestingly, this robustness originates in cell mechanics rather than biochemical networks. Highlights• Microtubule contacts at the cortex concentrate in regions close to the centrosomes.• This regulates pulling forces and creates a positional switch on oscillation onset.• The onset position resists changes in embryo length and force generator dynamics.• The final centrosome position resists changes in generator quantities and dynamics.not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/103937 doi: bioRxiv preprint first posted online Jan. 28, 2017; 3 Asymmetric cell divisions, with their differing daughter cell sizes, contents, and fates, are essential to the development of multicellular organisms 1,2 . As with many other species 3,4 , the mitotic spindle helps position the cytokinesis cleavage furrow in the nematode Caenorhabditis elegans 5 . To correspond to cortical polarity cues, the spindle needs to be oriented along the polarity axis 6 and displaced out of the cell centre before cytokinesis 6,7 . Most asymmetric division includes pulling forces from the cell cortex that are exerted on the astral microtubule plus ends, and these forces are key in positioning and orienting the spindle 6,7,8 .In the one-cell nematode embryo, c...

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“…Archiving and indexing large datasets is a nontrivial, but a possible task, as demonstrated by the plethora of database repositories currently in use for biology research, electron microscopy, microarray analysis, radiology, or multidiscipline research …”

Section: Introductionmentioning

confidence: 99%

Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline

González

Evans

2019

BioEssays

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Here, a streamlined, scalable, laboratory approach is discussed that enables medium‐to‐large dataset analysis. The presented approach combines data management, artificial intelligence, containerization, cluster orchestration, and quality control in a unified analytic pipeline. The unique combination of these individual building blocks creates a new and powerful analysis approach that can readily be applied to medium‐to‐large datasets by researchers to accelerate the pace of research. The proposed framework is applied to a project that counts the number of plasmonic nanoparticles bound to peripheral blood mononuclear cells in dark‐field microscopy images. By using the techniques presented in this article, the images are automatically processed overnight, without user interaction, streamlining the path from experiment to conclusions.

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Metadata management for high content screening in OMERO

Cited by 41 publications

References 34 publications

The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex

The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex

LET-99-dependent spatial restriction of active force generators makes spindle’s position robust

Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline

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