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Yang H, Nguyen AQ, Bi D, Buehler MJ, Guo M. Multicell-Fold: geometric learning in folding multicellular life. ARXIV 2024:arXiv:2407.07055v2. [PMID: 39040638 PMCID: PMC11261991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology. However, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. Here we present a geometric deep-learning model that can accurately capture the highly convoluted interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. Using this model, we achieve interpretable 4-D morphological sequence alignment, and predicting cell rearrangements before they occur at single-cell resolution. Furthermore, using neural activation map and ablation studies, we demonstrate cell geometries and cell junction networks together regulate morphogenesis at single-cell precision. This approach offers a pathway toward a unified dynamic atlas for a variety of developmental processes.
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Affiliation(s)
- Haiqian Yang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Anh Q. Nguyen
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Dapeng Bi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Markus J. Buehler
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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2
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Claussen NH, Brauns F, Shraiman BI. A Geometric Tension Dynamics Model of Epithelial Convergent Extension. ARXIV 2024:arXiv:2311.16384v2. [PMID: 38076522 PMCID: PMC10705598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Epithelial tissue elongation by convergent extension is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer under actively generated internal tension. To resolve this apparent paradox, we formulate a model in which tissue flow in the tension-dominated regime occurs through adiabatic remodeling of force balance in the network of adherens junctions. We propose that the slow dynamics within the manifold of force-balanced configurations is driven by positive feedback on myosin-generated cytoskeletal tension. Shifting force balance within a tension network causes active cell rearrangements (T1 transitions) resulting in net tissue deformation oriented by initial tension anisotropy. Strikingly, we find that the total extent of tissue deformation depends on the initial cellular packing order. T1s degrade this order so that tissue flow is self-limiting. We explain these findings by showing that coordination of T1s depends on coherence in local tension configurations, quantified by a geometric order parameter in tension space. Our model reproduces the salient tissue- and cell-scale features of germ band elongation during Drosophila gastrulation, in particular the slowdown of tissue flow after approximately twofold elongation concomitant with a loss of order in tension configurations. This suggests local cell geometry contains morphogenetic information and yields experimentally testable predictions. Furthermore, defining biologically controlled active tension dynamics on the manifold of force-balanced states may provide a general approach to the description of morphogenetic flow.
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Affiliation(s)
- Nikolas H. Claussen
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Fridtjof Brauns
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Boris I. Shraiman
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
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3
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Brauns F, Claussen NH, Lefebvre MF, Wieschaus EF, Shraiman BI. The Geometric Basis of Epithelial Convergent Extension. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.30.542935. [PMID: 37398061 PMCID: PMC10312603 DOI: 10.1101/2023.05.30.542935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Shape changes of epithelia during animal development, such as convergent extension, are achieved through concerted mechanical activity of individual cells. While much is known about the corresponding large scale tissue flow and its genetic drivers, fundamental questions regarding local control of contractile activity on cellular scale and its embryo-scale coordination remain open. To address these questions, we develop a quantitative, model-based analysis framework to relate cell geometry to local tension in recently obtained timelapse imaging data of gastrulating Drosophila embryos. This analysis provides a systematic decomposition of cell shape changes and T1-rearrangements into internally driven, active, and externally driven, passive, contributions. Our analysis provides evidence that germ band extension is driven by active T1 processes that self-organize through positive feedback acting on tensions. More generally, our findings suggest that epithelial convergent extension results from controlled transformation of internal force balance geometry which combines the effects of bottom-up local self-organization with the top-down, embryo-scale regulation by gene expression.
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Affiliation(s)
- Fridtjof Brauns
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Nikolas H. Claussen
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Matthew F. Lefebvre
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Eric F. Wieschaus
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Boris I. Shraiman
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
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4
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Sarkar T, Krajnc M. Graph topological transformations in space-filling cell aggregates. PLoS Comput Biol 2024; 20:e1012089. [PMID: 38743660 PMCID: PMC11093388 DOI: 10.1371/journal.pcbi.1012089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/19/2024] [Indexed: 05/16/2024] Open
Abstract
Cell rearrangements are fundamental mechanisms driving large-scale deformations of living tissues. In three-dimensional (3D) space-filling cell aggregates, cells rearrange through local topological transitions of the network of cell-cell interfaces, which is most conveniently described by the vertex model. Since these transitions are not yet mathematically properly formulated, the 3D vertex model is generally difficult to implement. The few existing implementations rely on highly customized and complex software-engineering solutions, which cannot be transparently delineated and are thus mostly non-reproducible. To solve this outstanding problem, we propose a reformulation of the vertex model. Our approach, called Graph Vertex Model (GVM), is based on storing the topology of the cell network into a knowledge graph with a particular data structure that allows performing cell-rearrangement events by simple graph transformations. Importantly, when these same transformations are applied to a two-dimensional (2D) polygonal cell aggregate, they reduce to a well-known T1 transition, thereby generalizing cell-rearrangements in 2D and 3D space-filling packings. This result suggests that the GVM's graph data structure may be the most natural representation of cell aggregates and tissues. We also develop a Python package that implements GVM, relying on a graph-database-management framework Neo4j. We use this package to characterize an order-disorder transition in 3D cell aggregates, driven by active noise and we find aggregates undergoing efficient ordering close to the transition point. In all, our work showcases knowledge graphs as particularly suitable data models for structured storage, analysis, and manipulation of tissue data.
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Affiliation(s)
- Tanmoy Sarkar
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matej Krajnc
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
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5
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Popkova A, Andrenšek U, Pagnotta S, Ziherl P, Krajnc M, Rauzi M. A mechanical wave travels along a genetic guide to drive the formation of an epithelial furrow during Drosophila gastrulation. Dev Cell 2024; 59:400-414.e5. [PMID: 38228140 DOI: 10.1016/j.devcel.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/08/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Epithelial furrowing is a fundamental morphogenetic process during gastrulation, neurulation, and body shaping. A furrow often results from a fold that propagates along a line. How fold formation and propagation are controlled and driven is poorly understood. To shed light on this, we study the formation of the cephalic furrow, a fold that runs along the embryo dorsal-ventral axis during Drosophila gastrulation and the developmental role of which is still unknown. We provide evidence of its function and show that epithelial furrowing is initiated by a group of cells. This cellular cluster works as a pacemaker, triggering a bidirectional morphogenetic wave powered by actomyosin contractions and sustained by de novo medial apex-to-apex cell adhesion. The pacemaker's Cartesian position is under the crossed control of the anterior-posterior and dorsal-ventral gene patterning systems. Thus, furrow formation is driven by a mechanical trigger wave that travels under the control of a multidimensional genetic guide.
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Affiliation(s)
- Anna Popkova
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
| | - Urška Andrenšek
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia; Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sophie Pagnotta
- Université Côte d'Azur, Centre Commun de Microscopie Appliquée, Nice, France
| | - Primož Ziherl
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia; Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matej Krajnc
- Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matteo Rauzi
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
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Clarke DN, Martin AC. EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573057. [PMID: 38187543 PMCID: PMC10769333 DOI: 10.1101/2023.12.22.573057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The movements that give rise to the body's structure are powered by cell shape changes and rearrangements that are coordinated at supracellular scales. How such cellular coordination arises and integrates different morphogenetic programs is unclear. Using quantitative imaging, we found a complex pattern of adherens junction (AJ) levels in the ectoderm prior to gastrulation onset in Drosophila. AJ intensity exhibited a double-sided gradient, with peaks at the dorsal midline and ventral neuroectoderm. We show that this dorsal-ventral AJ pattern is regulated by epidermal growth factor (EGF) signaling and that this signal is required for ectoderm cell movement during mesoderm invagination and axis extension. We identify AJ levels and junctional actomyosin as downstream effectors of EGFR signaling. Overall, our study demonstrates a mechanism of coordination between tissue folding and convergent extension that facilitates embryo-wide gastrulation movements.
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Affiliation(s)
| | - Adam C Martin
- Dept. of Biology, Massachusetts Institute of Technology
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Burda I, Martin AC, Roeder AHK, Collins MA. The dynamics and biophysics of shape formation: Common themes in plant and animal morphogenesis. Dev Cell 2023; 58:2850-2866. [PMID: 38113851 PMCID: PMC10752614 DOI: 10.1016/j.devcel.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023]
Abstract
The emergence of tissue form in multicellular organisms results from the complex interplay between genetics and physics. In both plants and animals, cells must act in concert to pattern their behaviors. Our understanding of the factors sculpting multicellular form has increased dramatically in the past few decades. From this work, common themes have emerged that connect plant and animal morphogenesis-an exciting connection that solidifies our understanding of the developmental basis of multicellular life. In this review, we will discuss the themes and the underlying principles that connect plant and animal morphogenesis, including the coordination of gene expression, signaling, growth, contraction, and mechanical and geometric feedback.
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Affiliation(s)
- Isabella Burda
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Genetic Genomics and Development Program, Cornell University, Ithaca, NY 14853, USA
| | - Adam C Martin
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Genetic Genomics and Development Program, Cornell University, Ithaca, NY 14853, USA; School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14850, USA.
| | - Mary Ann Collins
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Smits CM, Dutta S, Jain-Sharma V, Streichan SJ, Shvartsman SY. Maintaining symmetry during body axis elongation. Curr Biol 2023; 33:3536-3543.e6. [PMID: 37562404 DOI: 10.1016/j.cub.2023.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 06/29/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023]
Abstract
Bilateral symmetry defines much of the animal kingdom and is crucial for numerous functions of bilaterian organisms. Genetic approaches have discovered highly conserved patterning networks that establish bilateral symmetry in early embryos,1 but how this symmetry is maintained throughout subsequent morphogenetic events remains largely unknown.2 Here we show that the terminal patterning system-which relies on Ras/ERK signaling through activation of the Torso receptor by its ligand Trunk3-is critical for preserving bilateral symmetry during Drosophila body axis elongation, a process driven by cell rearrangements in the two identical lateral regions of the embryo and specified by the dorsal-ventral and anterior-posterior patterning systems.4 We demonstrate that fluctuating asymmetries in this rapid convergent-extension process are attenuated in normal embryos over time, possibly through noise-dissipating forces from the posterior midgut invagination and movement. However, when Torso signaling is attenuated via mutation of Trunk or RNAi directed against downstream Ras/ERK pathway components, body axis elongation results in a characteristic corkscrew phenotype,5 which reflects dramatic reorganization of global tissue flow and is incompatible with viability. Our results reveal a new function downstream of the Drosophila terminal patterning system in potentially active control of bilateral symmetry and should motivate systematic search for similar symmetry-preserving regulatory mechanisms in other bilaterians.
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Affiliation(s)
- Celia M Smits
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Sayantan Dutta
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Vishank Jain-Sharma
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Sebastian J Streichan
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
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9
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Godivier J, Lawrence EA, Wang M, Hammond CL, Nowlan NC. Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish. J Anat 2022; 241:358-371. [PMID: 35510779 PMCID: PMC9296026 DOI: 10.1111/joa.13680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
In early limb embryogenesis, synovial joints acquire specific shapes which determine joint motion and function. The process by which the opposing cartilaginous joint surfaces are moulded into reciprocal and interlocking shapes, called joint morphogenesis, is one of the least understood aspects of joint formation and the cell-level dynamics underlying it are yet to be unravelled. In this research, we quantified key cellular dynamics involved in growth and morphogenesis of the zebrafish jaw joint and synthesised them in a predictive computational simulation of joint development. Cells in larval zebrafish jaw joints labelled with cartilage markers were tracked over a 48-h time window using confocal imaging. Changes in distance and angle between adjacent cell centroids resulting from cell rearrangement, volume expansion and extracellular matrix (ECM) deposition were measured and used to calculate the rate and direction of local tissue deformations. We observed spatially and temporally heterogeneous growth patterns with marked anisotropy over the developmental period assessed. There was notably elevated growth at the level of the retroarticular process of the Meckel's cartilage, a feature known to undergo pronounced shape changes during zebrafish development. Analysis of cell dynamics indicated a dominant role for cell volume expansion in growth, with minor influences from ECM volume increases and cell intercalation. Cell proliferation in the joint was minimal over the timeframe of interest. Synthesising the dynamic cell data into a finite element model of jaw joint development resulted in accurate shape predictions. Our biofidelic computational simulation demonstrated that zebrafish jaw joint growth can be reasonably approximated based on cell positional information over time, where cell positional information derives mainly from cell orientation and cell volume expansion. By modifying the input parameters of the simulation, we were able to assess the relative contributions of heterogeneous growth rates and of growth orientation. The use of uniform rather than heterogeneous growth rates only minorly impacted the shape predictions, whereas isotropic growth fields resulted in altered shape predictions. The simulation results suggest that growth anisotropy is the dominant influence on joint growth and morphogenesis. This study addresses the gap of the cellular processes underlying joint morphogenesis, with implications for understanding the aetiology of developmental joint disorders such as developmental dysplasia of the hip and arthrogryposis.
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Affiliation(s)
| | | | | | | | - Niamh C. Nowlan
- Imperial College LondonLondonUnited Kingdom,University College DublinDublinIreland
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Camuglia J, Chanet S, Martin AC. Morphogenetic forces planar polarize LGN/Pins in the embryonic head during Drosophila gastrulation. eLife 2022; 11:78779. [PMID: 35796436 PMCID: PMC9262390 DOI: 10.7554/elife.78779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/05/2022] [Indexed: 01/03/2023] Open
Abstract
Spindle orientation is often achieved by a complex of Partner of Inscuteable (Pins)/LGN, Mushroom Body Defect (Mud)/Nuclear Mitotic Apparatus (NuMa), Gαi, and Dynein, which interacts with astral microtubules to rotate the spindle. Cortical Pins/LGN recruitment serves as a critical step in this process. Here, we identify Pins-mediated planar cell polarized divisions in several of the mitotic domains of the early Drosophila embryo. We found that neither planar cell polarity pathways nor planar polarized myosin localization determined division orientation; instead, our findings strongly suggest that Pins planar polarity and force generated from mesoderm invagination are important. Disrupting Pins polarity via overexpression of a myristoylated version of Pins caused randomized division angles. We found that disrupting forces through chemical inhibitors, depletion of an adherens junction protein, or blocking mesoderm invagination disrupted Pins planar polarity and spindle orientation. Furthermore, directional ablations that separated mesoderm from mitotic domains disrupted spindle orientation, suggesting that forces transmitted from mesoderm to mitotic domains can polarize Pins and orient division during gastrulation. To our knowledge, this is the first in vivo example where mechanical force has been shown to polarize Pins to mediate division orientation.
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Affiliation(s)
- Jaclyn Camuglia
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Soline Chanet
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Adam C Martin
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, United States
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EmbedSeg: Embedding-based Instance Segmentation for Biomedical Microscopy Data. Med Image Anal 2022; 81:102523. [DOI: 10.1016/j.media.2022.102523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/02/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
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