Nu3D: 3D Nuclei Segmentation from Light-Sheet Microscopy Images of the Embryonic Heart

Author(s):  
Rituparna Sarkar ◽  
Daniel Darby ◽  
Heloise Foucambert ◽  
Sigolene Meilhac ◽  
Jean-Christophe Olivo-Marin
2018 ◽  
Author(s):  
Meghan K. Driscoll ◽  
Erik S. Welf ◽  
Kevin M. Dean ◽  
Reto Fiolka ◽  
Gaudenz Danuser

AbstractRecent advances in light-sheet microscopy enable imaging of cell morphology and signaling with unprecedented detail. However, the analytical tools to systematically measure and visualize the intricate relations between cell morphodynamics, intracellular signaling, and cytoskeletal dynamics have been largely missing. Here, we introduce a set of computer vision and graphics methods to dissect molecular mechanisms underlying 3D cell morphogenesis and to test whether morphogenesis itself affects intracellular signaling. We demonstrate a machine learning based generic morphological motif detector that automatically finds lamellipodia, filopodia, and blebs on various cell types. Combining motif detection with molecular localization, we measure the differential association of PIP2 and KrasV12 with blebs. Both signals associate with bleb edges, as expected for membrane-localized proteins, but only PIP2 is enhanced on blebs. This suggests that local morphological cues differentially organize and activate sub-cellular signaling processes. Overall, our computational workflow enables the objective, automated analysis of the 3D coupling of morphodynamics with cytoskeletal dynamics and intracellular signaling.


2014 ◽  
Vol 30 (17) ◽  
pp. i587-i593 ◽  
Author(s):  
Paolo Frasconi ◽  
Ludovico Silvestri ◽  
Paolo Soda ◽  
Roberto Cortini ◽  
Francesco S. Pavone ◽  
...  

2015 ◽  
Vol 6 (6) ◽  
pp. 2056 ◽  
Author(s):  
Vikas Trivedi ◽  
Thai V. Truong ◽  
Le A. Trinh ◽  
Daniel B. Holland ◽  
Michael Liebling ◽  
...  

2011 ◽  
Vol 17 (4) ◽  
pp. 607-613 ◽  
Author(s):  
Mohammad Shorif Uddin ◽  
Hwee Kuan Lee ◽  
Stephan Preibisch ◽  
Pavel Tomancak

AbstractLight microscopy images suffer from poor contrast due to light absorption and scattering by the media. The resulting decay in contrast varies exponentially across the image along the incident light path. Classical space invariant deconvolution approaches, while very effective in deblurring, are not designed for the restoration of uneven illumination in microscopy images. In this article, we present a modified radiative transfer theory approach to solve the contrast degradation problem of light sheet microscopy (LSM) images. We confirmed the effectiveness of our approach through simulation as well as real LSM images.


2017 ◽  
Author(s):  
Bálint Balázs ◽  
Joran Deschamps ◽  
Marvin Albert ◽  
Jonas Ries ◽  
Lars Hufnagel

AbstractFluorescence imaging techniques such as single molecule localization microscopy, high-content screening and light-sheet microscopy are producing ever-larger datasets, which poses increasing challenges in data handling and data sharing. Here, we introduce a real-time compression library that allows for very fast (beyond 1 GB/s) compression and de-compression of microscopy datasets during acquisition. In addition to an efficient lossless mode, our algorithm also includes a lossy option, which limits pixel deviations to the intrinsic noise level of the image and yields compression ratio of up to 100-fold. We present a detailed performance analysis of the different compression modes for various biological samples and imaging modalities.


Nanophotonics ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Qingqing Cheng ◽  
Juncheng Wang ◽  
Ling Ma ◽  
Zhixiong Shen ◽  
Jing Zhang ◽  
...  

AbstractAiry beams exhibit intriguing properties such as nonspreading, self-bending, and self-healing and have attracted considerable recent interest because of their many potential applications in photonics, such as to beam focusing, light-sheet microscopy, and biomedical imaging. However, previous approaches to generate Airy beams using photonic structures have suffered from severe chromatic problems arising from strong frequency dispersion of the scatterers. Here, we design and fabricate a metasurface composed of silicon posts for the frequency range 0.4–0.8 THz in transmission mode, and we experimentally demonstrate achromatic Airy beams exhibiting autofocusing properties. We further show numerically that a generated achromatic Airy-beam-based metalens exhibits self-healing properties that are immune to scattering by particles and that it also possesses a larger depth of focus than a traditional metalens. Our results pave the way to the realization of flat photonic devices for applications to noninvasive biomedical imaging and light-sheet microscopy, and we provide a numerical demonstration of a device protocol.


2021 ◽  
Vol 93 (8) ◽  
pp. 4092-4099
Author(s):  
Bing Li ◽  
Aleks Ponjavic ◽  
Wei-Hsin Chen ◽  
Lee Hopkins ◽  
Craig Hughes ◽  
...  

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