accurate and versatile 3d segmentation of plant tissues at

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Accurate and Versatile 3D Segmentation of Plant Tissues at ...

2020-1-18  Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution Adrian Wolny, Lorenzo Cerrone, Athul Vijayan, Rachele Tofanelli, Amaya Vilches Barro, Marion Louveaux, Christian Wenzl, Susanne Steigleder, Constantin Pape, Alberto Bailoni, Salva Duran-Nebreda, George Bassel, Jan U. Lohmann, Fred A. Hamprecht,

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Accurate and versatile 3D segmentation of plant tissues at ...

2020-7-29  Accurate and versatile extraction of cell outlines rendered possible by PlantSeg opens the door to rapid and robust quantitative morphometric analysis of plant cell geometry in complex tissues. This is particularly relevant given the central role plant cell shape plays in the control of cell growth and division ( Rasmussen and Bellinger, 2018 ).

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Accurate and versatile 3D segmentation of plant tissues at ...

Accurate and versatile 3D segmentation of plant tissues at cellular resolution Adrian Wolny1,2†, Lorenzo Cerrone1†, Athul Vijayan3, Rachele Tofanelli3, Amaya Vilches Barro4, Marion Louveaux4‡, Christian Wenzl4, So¨ren Strauss5, David Wilson-Sa´nchez5, Rena Lymbouridou5, Susanne S Steigleder4,

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Accurate and versatile 3D segmentation of plant tissues at ...

2020-7-29  Segmentation of plant tissues into cells using PlantSeg. First, PlantSeg uses a 3D UNet neural network to predict the boundaries between cells. Second, a volume partitioning algorithm is applied to segment each cell based on the predicted boundaries.

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Accurate and versatile 3D segmentation of plant tissues at ...

2020-7-29  PlantSeg, a simple, powerful, and versatile tool for plant cell segmentation. Internally, it implements. a two-step algorithm: the images are first passed through a state-of-the-art convolutional ...

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Accurate and versatile 3D segmentation of plant tissues at ...

2020-3-31  Accurate and versatile 3D segmentation of plant tissues at cellular resolution: Core Datasets ... Accurate and versatile 3D segmentation of plant tissues at cellular resolution: Core Datasets. 0.0B. ... Repository containing 2 core datasets of fixed and live plant organs imaged with confocal and light sheet microscopes together with ground ...

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Accurate and versatile 3D segmentation of plant tissues at ...

2020-3-31  Adrian Wolny updated wiki page Home to version 5 of Accurate and versatile 3D segmentation of plant tissues at cellular resolution: Core Datasets 2020-04-13 11:21 AM 1

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Accurate and versatile 3D segmentation of plant tissues at ...

Author: Wolny, A. et al.; Genre: Journal Article; Published online: 2020; Open Access; Title: Accurate and versatile 3D segmentation of plant tissues at cellular ...

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Segmentation of 3D images of plant tissues at multiple ...

2017-12-21  Segmentation of 3D images of plant tissues at multiple scales using the level set method. Kiss A(1), Moreau T(1), Mirabet V(1), Calugaru CI(2), Boudaoud A(1), Das P(1). Author information: (1)Laboratoire Reproduction et Développement des Plantes, Univ Lyon, UCB Lyon 1, ENS de Lyon, CNRS, INRA, 46, allée d'Italie, 69342 Lyon, France.

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David Wilson-Sánchez Papers With Code

Accurate and versatile 3D segmentation of plant tissues at cellular resolution. ... Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. Cell Segmentation graph partitioning. 39.

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GitHub - wolny/pytorch-3dunet: 3D U-Net model for ...

@article {10.7554/eLife.57613, article_type = {journal}, title = {Accurate and versatile 3D segmentation of plant tissues at cellular resolution}, author = {Wolny, Adrian and Cerrone, Lorenzo and Vijayan, Athul and Tofanelli, Rachele and Barro, Amaya Vilches and

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Segmentation of 3D images of plant tissues at multiple ...

2017-12-21  A key challenge in generalising such an approach to assess developmental trajectories for 3D tissues is the detection of accurate tissue contours, which our tool efficiently achieves. Segmentation at the cellular level is useful to properly describe tissue structure, and to correlate genetic activity, via reporter expression, to cell ...

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Publications Heidelberg Collaboratory for Image ...

2021-8-14  Accurate and versatile 3D segmentation of plant tissues at cellular resolution. eLife. DOI; Google Scholar; BibTeX; RTF; EndNote XML; Haußmann, M, Gerwinn, S and Kandemir, M (2020). Bayesian Evidential Deep Learning with PAC Regularization . 3rd Symposium on Advances in Approximate Bayesian Inference . Google Scholar; BibTeX; RTF; EndNote XML

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TUM Professoren - Schneitz_Kay Heinrich

Wolny A, Cerrone L, Vijayan A, Tofanelli R, Vilches Barro A, Louveaux M, Wenzl C, Strauss S, Wilson-Sánchez D, Lymbouridou R, Steigleder S, Pape C, Bailoni A, Duran-Nebreda S, Bassel G, Lohmann J, Tsiantis M, Hamprecht FA, Schneitz K, Maizel A and Kreshuk A: “Accurate and versatile 3D segmentation of plant tissues at

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Analysing Plant Cells With 3D Images – Heidelberg University

“PlantSeg now lets us study plant tissues with extreme precision. We hope it will give us a better understanding of speciation processes and how plants react to changing environmental conditions,” explains Prof. Maizel. ... M. Tsiantis, F. Hamprecht, K. Schneitz, A. Maizel, A. Kreshuk: Accurate and versatile 3D segmentation of plant tissues ...

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‪Constantin Pape‬ - ‪Google Scholar‬

Accurate and versatile 3D segmentation of plant tissues at cellular resolution A Wolny, L Cerrone, A Vijayan, R Tofanelli, AV Barro, M Louveaux, ... Elife 9, e57613 , 2020

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Intelligent software tackles plant cell jigsaw puzzle

2020-8-31  More information: Adrian Wolny et al, Accurate and versatile 3D segmentation of plant tissues at cellular resolution, eLife (2020). DOI: 10.7554/eLife.57613 Journal information: eLife

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Deep Residual 3D U-Net for Joint Segmentation and Texture ...

2020-6-17  Clevert, D. A., Unterthiner, T., Hochreiter, S.: Fast and accurate deep network learning by Exponential Linear ... Kreshuk, A.: Accurate and versatile 3D segmentation of plant tissues at cellular resolution. bioRxiv ... Rassadin A. (2020) Deep Residual 3D U-Net for Joint Segmentation and Texture Classification of Nodules in Lung. In: Campilho A ...

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GitHub - DiamondLightSource/gas-hydrate-segmentation

And the 3d U-net utilises the pytorch-3dunet library: Wolny, Adrian, Lorenzo Cerrone, Athul Vijayan, Rachele Tofanelli, Amaya Vilches Barro, Marion Louveaux, Christian Wenzl, et al. ‘Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution’. Edited by Christian S Hardtke, Dominique C Bergmann, Dominique C Bergmann, and ...

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Intelligent software tackles plant cell jigsaw puzzle ...

2020-8-31  The group has trained PlantSeg on many plant tissue volumes, so that now it generalises quite well to unseen plant data. ... Accurate and versatile 3D segmentation of plant tissues at cellular ...

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Segmentation of 3D images of plant tissues at multiple ...

2017-12-21  A key challenge in generalising such an approach to assess developmental trajectories for 3D tissues is the detection of accurate tissue contours, which our tool efficiently achieves. Segmentation at the cellular level is useful to properly describe tissue structure, and to correlate genetic activity, via reporter expression, to cell ...

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Unsupervised deep learning method for cell segmentation

2021-5-17  Accurate and versatile 3D segmentation of plant tissues at cellular 347 resolution ... Wolny, A. et al. Accurate and versatile 3D segmentation of plant tissues at cellular 347 resolution. eLife 9 ...

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Segmentation of 3D images of plant tissues at multiple ...

2017-12-21  Segmentation of 3D images of plant tissues at multiple scales using the level set method. Kiss A(1), Moreau T(1), Mirabet V(1), Calugaru CI(2), Boudaoud A(1), Das P(1). Author information: (1)Laboratoire Reproduction et Développement des Plantes, Univ Lyon, UCB Lyon 1, ENS de Lyon, CNRS, INRA, 46, allée d'Italie, 69342 Lyon, France.

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Deep Residual 3D U-Net for Joint Segmentation and Texture ...

2020-6-17  Clevert, D. A., Unterthiner, T., Hochreiter, S.: Fast and accurate deep network learning by Exponential Linear ... Kreshuk, A.: Accurate and versatile 3D segmentation of plant tissues at cellular resolution. bioRxiv ... Rassadin A. (2020) Deep Residual 3D U-Net for Joint Segmentation and Texture Classification of Nodules in Lung. In: Campilho A ...

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‪Anna Kreshuk‬ - ‪Google Scholar‬

Accurate and versatile 3D segmentation of plant tissues at cellular resolution A Wolny, L Cerrone, A Vijayan, R Tofanelli, AV Barro, M Louveaux, ... Elife 9, e57613 , 2020

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Revealing the spatio-phenotypic patterning of cells in ...

2021-6-3  Wolny, A. et al. Accurate and versatile 3D segmentation of plant tissues at cellular resolution. Elife 9 , 1–34 (2020). Article Google Scholar

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Intelligent software tackles plant cell jigsaw Mirage News

2020-8-31  Adrian Wolny et al. Accurate and versatile 3D segmentation of plant tissues at cellular resolution. eLifeSciences, published online 29 July 2020; DOI: 10.7554/eLife.57613 Related links EMBL is bridging AI and life sciences in new ways with ELLIS

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TUM Professoren - Schneitz_Kay Heinrich

Wolny A, Cerrone L, Vijayan A, Tofanelli R, Vilches Barro A, Louveaux M, Wenzl C, Strauss S, Wilson-Sánchez D, Lymbouridou R, Steigleder S, Pape C, Bailoni A, Duran-Nebreda S, Bassel G, Lohmann J, Tsiantis M, Hamprecht FA, Schneitz K, Maizel A and Kreshuk A: “Accurate and versatile 3D segmentation of plant tissues at cellular resolution”.

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[PDF] Leveraging Domain Knowledge to Improve Microscopy ...

The throughput of electron microscopes has increased significantly in recent years, enabling detailed analysis of cell morphology and ultrastructure. Analysis of neural circuits at single-synapse resolution remains the flagship target of this technique, but applications to cell and developmental biology are also starting to emerge at scale. The amount of data acquired in such studies makes ...

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