Image analysis for understanding embryo development: a bridge from microscopy to biological insights

Luengo-Oroz, Miguel; Ledesma-Carbayo, María J.; Peyriéras, Nadine; Santos, A.

doi:10.1016/j.gde.2011.08.001

Cited by 33 publications

(37 citation statements)

References 55 publications

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“…The THG signal highlights membrane geometry and is used to segment the cell shape. A typical acquisition is in the order of 100 volumes of size (512, 512, 120) with voxel size of (2, 2, 4) |im 3 and AT = 90 s.…”

Section: Overview Of Processing Methodsmentioning

confidence: 99%

Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy

Luengo-Oroz

Rubio-Guivernau

Faure

et al. 2012

IEEE Trans. on Image Process.

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Abstract-Investigating cell dynamics during early zebraflsh embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second-and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebraflsh embryos from 1-to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebraflsh embryogenesis.Index Terms-Cell lineage tree, in vivo 4-D imaging, multiphoton microscopy, viscous watershed, zebraflsh.

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Section: Overview Of Processing Methodsmentioning

confidence: 99%

Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy

Luengo-Oroz

Rubio-Guivernau

Faure

et al. 2012

IEEE Trans. on Image Process.

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“…Finally, the artificial gene expression was created following a smoothed "on-off" propagation model, which affects different cell volumes through time. As a result, we generated an artificial model with spatial resolution 0.52 x 0.52 x 1.04 jum 3 and temporal resolution At = 1 min 21 s comprising 21 frames of 512 x 512 x 128 voxels. At first, there are 14 nuclei, which undergo at least one mitosis each, most of them synchronously, yielding a total of 29 cells by the end of the experiment (see Fig.…”

Section: A Synthetic Embryogenetic Datasetmentioning

confidence: 99%

“…We have first downsampled our synthetic dataset to make it spatially isotropic -1.04 x 1.04 x 1.04 ¿¿m 3 . Then, we have contaminated the artificial membranes with uncorrelated Gaussian noise of mean 0 and SNR 3.7 dB.…”

Section: B Twister Filtering For Oriented Hyper-structures 1) Descrimentioning

confidence: 99%

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<formula formulatype="inline"><tex Notation="TeX">$3D+t$</tex></formula> Morphological Processing: Applications to Embryogenesis Image Analysis

Luengo-Oroz

Pastor-Escuredo

Castro-González

et al. 2012

IEEE Trans. on Image Process.

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Abstract-Wepropose to directly process 3D+t image sequences with mathematical morphology operators, using a new classification of the 3D + t structuring elements. Several methods (filtering, tracking, segmentation) dedicated to the analysis of 3D +1 datasets of zebrafish embryogenesis are introduced and validated through a synthetic dataset. Then, we illustrate the application of these methods to the analysis of datasets of zebrafish early development acquired with various microscopy techniques. This processing paradigm produces spatio-temporal coherent results as it benefits from the intrinsic redundancy of the temporal dimension, and minimizes the needs for human intervention in semi-automatic algorithms.Index Terms-3D +t mathematical morphology, in-vivo light microscopy, spatio-temporal structuring elements, zebrafish embryogenesis.

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“…5 Imaging approaches include three-dimensional time lapse (3D + t) imaging of embryos by confocal or multiphoton laser scanning microscopy, which generates different signals for image analysis, including two-photon-excited fluorescence, second harmonic generation (SHG), and third harmonic generation (THG). 6 Another technique used in 3D + t imaging is selective plane illumination microscopy (SPIM), 7 which is also called light sheet fluorescence microscopy (LSFM). In addition, video series are recorded to observe developmental or behavioral changes over longer periods of time in larvae and adults.…”

Section: Introductionmentioning

confidence: 99%

Automated Processing of Zebrafish Imaging Data: A Survey

et al. 2013

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Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for highthroughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.

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Image analysis for understanding embryo development: a bridge from microscopy to biological insights

Cited by 33 publications

References 55 publications

Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy

Methodology for Reconstructing Early Zebrafish Development From In Vivo Multiphoton Microscopy

<formula formulatype="inline"><tex Notation="TeX">$3D+t$</tex></formula> Morphological Processing: Applications to Embryogenesis Image Analysis

Automated Processing of Zebrafish Imaging Data: A Survey

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