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101 Research products

  • Neuroinformatics
  • Open Access
  • European Commission
  • EC|HE

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Lim, Soon Hoe; Wan, Yijun; Şimşekli, Umut;

    Recent studies have shown that gradient descent (GD) can achieve improved generalization when its dynamics exhibits a chaotic behavior. However, to obtain the desired effect, the step-size should be chosen sufficiently large, a task which is problem dependent and can be difficult in practice. In this study, we incorporate a chaotic component to GD in a controlled manner, and introduce multiscale perturbed GD (MPGD), a novel optimization framework where the GD recursion is augmented with chaotic perturbations that evolve via an independent dynamical system. We analyze MPGD from three different angles: (i) By building up on recent advances in rough paths theory, we show that, under appropriate assumptions, as the step-size decreases, the MPGD recursion converges weakly to a stochastic differential equation (SDE) driven by a heavy-tailed L\'evy-stable process. (ii) By making connections to recently developed generalization bounds for heavy-tailed processes, we derive a generalization bound for the limiting SDE and relate the worst-case generalization error over the trajectories of the process to the parameters of MPGD. (iii) We analyze the implicit regularization effect brought by the dynamical regularization and show that, in the weak perturbation regime, MPGD introduces terms that penalize the Hessian of the loss function. Empirical results are provided to demonstrate the advantages of MPGD. Comment: 24 pages, accepted at NeurIPS 2022

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
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    https://doi.org/10.48550/arxiv...
    Article . 2022
    License: CC BY
    Data sources: Datacite
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    Other literature type . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: R Varennes; X Garbet; L Vermare; Y Sarazin; +7 Authors

    Abstract The effect of magnetic field ripple on tokamak plasma without turbulence is studied numerically and augmented with a reduced analytical model that includes neoclassical processes in the presence of non-axisymmetric perturbation and stochastic transport. For this study, a magnetic field ripple perturbation has been implemented in the GYSELA gyrokinetic code. This implementation has been verified thanks to a test of toroidal angular momentum conservation. The GYSELA code was then successfully benchmarked against the NEO code, which solves the drift kinetic equation, and against the reduced model in the collisionality range ν ⋆ ∈ [0.05–0.5] for several amplitudes of the magnetic ripple. An observation, shared by the model, the NEO code and GYSELA simulations is that the thermal drive of the mean poloidal velocity—measured by the k V P coefficient—decreases sharply for large yet experimentally relevant magnetic ripple amplitudes, and may even change sign.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Plasma Physics and Controlled Fusion
    Article . 2023 . Peer-reviewed
    License: IOP Copyright Policies
    Data sources: Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hyper Article en Lig...arrow_drop_down
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Plasma Physics and Controlled Fusion
      Article . 2023 . Peer-reviewed
      License: IOP Copyright Policies
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Babak Rezaei; Jessica Giacomoni; Fredrik Nilsson; Edoardo Sozzi; +4 Authors

    Abstract Brain organoid technology has transformed both basic and applied biomedical research and paved the way for novel insights into developmental processes and disease states of the human brain. While the use of brain organoids has been rapidly growing in the past decade, the accompanying bioengineering and biofabrication solutions have remained scarce. As a result, most brain organoid protocols still rely on commercially available tools and culturing platforms that had previously been established for different purposes, thus entailing suboptimal culturing conditions and excessive use of plasticware. To address these issues, we developed a 3D printing pipeline for the fabrication of tailor-made culturing platforms for fluidically connected but spatially separated brain organoid array culture. This all-in-one platform allows all culturing steps—from cellular aggregation, spheroid growth, hydrogel embedding, and organoid maturation—to be performed in a single well plate without the need for organoid manipulation or transfer. Importantly, the approach relies on accessible materials and widely available 3D printing equipment. Furthermore, the developed design principles are modular and highly customizable. As such, we believe that the presented technology can be easily adapted by other research groups and fuel further development of culturing tools and platforms for brain organoids and other 3D cellular systems.

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    Biofabrication
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Biofabrication
    Article . 2023
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      Biofabrication
      Article . 2023 . Peer-reviewed
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      Biofabrication
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Varennes, R.; Garbet, X.; Vermare, L.; Sarazin, Y.; +7 Authors

    In absence of external torque, plasma rotation in tokamaks results from a balance between collisional magnetic braking and turbulent drive. The outcome of this competition and cooperation is essential to determine the plasma flow. A reduced model, supported by gyrokinetic simulations, is first used to explain and quantify the competition only. The ripple amplitude above which magnetic drag overcomes turbulent viscosity is obtained. The synergetic impact of ripple on the turbulent toroidal Reynolds stress is explored. Simulations show that the main effect comes from an enhancement of the radial electric field shear by the ripple, which in turn impacts the residual stress.

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Physical Review Letters
    Article . 2022 . Peer-reviewed
    License: APS Licenses for Journal Article Re-use
    Data sources: Sygma; Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hyper Article en Lig...arrow_drop_down
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Physical Review Letters
      Article . 2022 . Peer-reviewed
      License: APS Licenses for Journal Article Re-use
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Neumann, Wolf-Julian; Horn, Andreas; Kühn, Andrea A.;

    Deep brain stimulation (DBS) is an effective treatment and has provided unique insights into the dynamic circuit architecture of brain disorders. This Review illustrates our current understanding of the pathophysiology of movement disorders and their underlying brain circuits that are modulated with DBS. It proposes principles of pathological network synchronization patterns like beta activity (13-35 Hz) in Parkinson's disease. We describe alterations from microscale including local synaptic activity via modulation of mesoscale hypersynchronization to changes in whole-brain macroscale connectivity. Finally, an outlook on advances for clinical innovations in next-generation neurotechnology is provided: from preoperative connectomic targeting to feedback controlled closed-loop adaptive DBS as individualized network-specific brain circuit interventions.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Trends in Neuroscien...arrow_drop_down
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    Trends in Neurosciences
    Article . 2023 . Peer-reviewed
    License: Elsevier TDM
    Data sources: Sygma; Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Trends in Neuroscien...arrow_drop_down
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      Trends in Neurosciences
      Article . 2023 . Peer-reviewed
      License: Elsevier TDM
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    Authors: Rachele Fabbri; Ludovica Cacopardo; Arti Ahluwalia; Chiara Magliaro;

    Human-relevant three-dimensional (3D) models of cerebral tissue can be invaluable tools to boost our understanding of the cellular mechanisms underlying brain pathophysiology. Nowadays, the accessibility, isolation and harvesting of human neural cells represents a bottleneck for obtaining reproducible and accurate models and gaining insights in the fields of oncology, neurodegenerative diseases and toxicology. In this scenario, given their low cost, ease of culture and reproducibility, neural cell lines constitute a key tool for developing usable and reliable models of the human brain. Here, we review the most recent advances in 3D constructs laden with neural cell lines, highlighting their advantages and limitations and their possible future applications.

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    Cells
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Cells
    Article . 2023
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      Cells
      Article . 2023 . Peer-reviewed
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      Cells
      Article . 2023
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    Authors: Siemon C. de Lange; Koen Helwegen; Martijn P. van den Heuvel;

    We describe a Connectivity Analysis TOolbox (CATO) for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging and resting-state functional MRI data. CATO is a multimodal software package that enables researchers to run end-to-end reconstructions from MRI data to structural and functional connectome maps, customize their analyses and utilize various software packages to preprocess data. Structural and functional connectome maps can be reconstructed with respect to user-defined (sub)cortical atlases providing aligned connectivity matrices for integrative multimodal analyses. We outline the implementation and usage of the structural and functional processing pipelines in CATO. Performance was calibrated with respect to simulated diffusion weighted imaging data from the ITC2015 challenge and test-retest diffusion weighted imaging data and resting-state functional MRI data from the Human Connectome Project. CATO is open-source software distributed under the MIT License and available as a MATLAB toolbox and as a stand-alone application at www.dutchconnectomelab.nl/CATO.

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    NARCIS; NeuroImage
    Article . 2023
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    NeuroImage
    Article . 2022
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    NARCIS
    Article . 2023
    Data sources: NARCIS
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      NARCIS; NeuroImage
      Article . 2023
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      NeuroImage
      Article . 2022
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      NARCIS
      Article . 2023
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    Authors: Jan Peszek; David Poyato;

    We introduce an optimal transport topology on the space of probability measures over a fiber bundle, which penalizes the transport cost from one fiber to another. For simplicity, we illustrate our construction in the Euclidean case $\mathbb{R}^d\times \mathbb{R}^d$, where we penalize the quadratic cost in the second component. Optimal transport becomes then constrained to happen along fixed fibers. Despite the degeneracy of the infinitely-valued and discontinuous cost, we prove that the space of probability measures $(\mathcal{P}_{2,\nu}(\mathbb{R}^{2d}),W_{2,\nu})$ with fixed marginal $\nu\in \mathcal{P}(\mathbb{R}^d)$ in the second component becomes a Polish space under the fibered transport distance, which enjoys a weak Riemannian structure reminiscent of the one proposed by F. Otto for the classical quadratic Wasserstein space. Three fundamental issues are addressed: 1) We develop an abstract theory of gradient flows with respect to the new topology; 2) We show applications that identify a novel fibered gradient flow structure on a large class of evolution PDEs with heterogeneities; 3) We exploit our method to derive long-time behavior and global-in-time mean-field limits in a multidimensional Cucker-Smale-type alignment model with weakly singular coupling. Comment: 59 pages

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    Calculus of Variations and Partial Differential Equations
    Article . 2023 . Peer-reviewed
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      Calculus of Variations and Partial Differential Equations
      Article . 2023 . Peer-reviewed
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    Authors: Célia Griffet; Matthieu Arnhem; Stephan De Bièvre; Nicolas J. Cerf;

    Assessing whether a quantum state $\hat \rho$ is nonclassical ($\textit{i.e.}$, incompatible with a mixture of coherent states) is a ubiquitous question in quantum optics, yet a nontrivial experimental task because many nonclassicality witnesses are nonlinear in $\hat \rho$. In particular, if we want to witness or measure the nonclassicality of a state by evaluating its quadrature coherence scale, this $\textit{a priori}$ requires full state tomography. Here, we provide an experimental procedure for directly accessing this quantity with a simple linear interferometer involving two replicas (independent and identical copies) of the state $\hat \rho$ supplemented with photon-number-resolving measurements. This finding, which we interpret as an extension of the Hong-Ou-Mandel effect, illustrates the wide applicability of the multicopy interferometric technique in order to circumvent state tomography in quantum optics. Comment: Minor corrections in v2 to match the published version of the paper, 12 pages, 3 figures,

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    Lille Open Archive
    Review . 2023
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    https://doi.org/10.1103/physre...
    Article . 2023 . Peer-reviewed
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      Lille Open Archive
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      https://doi.org/10.1103/physre...
      Article . 2023 . Peer-reviewed
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    Authors: Crestetto, Anaïs; Crouseilles, Nicolas; Prel, Damien;

    This work is devoted to the construction of multiscale numerical schemes efficient in the finite Larmor radius approximation of the collisional Vlasov equation. Following the paper of Bostan and Finot (2019), the system involves two different regimes, a highly oscillatory and a dissipative regimes, whose asymptotic limits do not commute. In this work, we consider a Particle-In-Cell discretization of the collisional Vlasov system which enables to deal with the multiscale characteristics equations. Different multiscale time integrators are then constructed and analysed. We prove asymptotic properties of these schemes in the highly oscillatory regime and in the collisional regime. In particular, the asymptotic preserving property towards the modified equilibrium of the averaged collision operator is recovered. Numerical experiments are then shown to illustrate the properties of the numerical schemes.

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101 Research products
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Lim, Soon Hoe; Wan, Yijun; Şimşekli, Umut;

    Recent studies have shown that gradient descent (GD) can achieve improved generalization when its dynamics exhibits a chaotic behavior. However, to obtain the desired effect, the step-size should be chosen sufficiently large, a task which is problem dependent and can be difficult in practice. In this study, we incorporate a chaotic component to GD in a controlled manner, and introduce multiscale perturbed GD (MPGD), a novel optimization framework where the GD recursion is augmented with chaotic perturbations that evolve via an independent dynamical system. We analyze MPGD from three different angles: (i) By building up on recent advances in rough paths theory, we show that, under appropriate assumptions, as the step-size decreases, the MPGD recursion converges weakly to a stochastic differential equation (SDE) driven by a heavy-tailed L\'evy-stable process. (ii) By making connections to recently developed generalization bounds for heavy-tailed processes, we derive a generalization bound for the limiting SDE and relate the worst-case generalization error over the trajectories of the process to the parameters of MPGD. (iii) We analyze the implicit regularization effect brought by the dynamical regularization and show that, in the weak perturbation regime, MPGD introduces terms that penalize the Hessian of the loss function. Empirical results are provided to demonstrate the advantages of MPGD. Comment: 24 pages, accepted at NeurIPS 2022

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    https://doi.org/10.48550/arxiv...
    Article . 2022
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    Authors: R Varennes; X Garbet; L Vermare; Y Sarazin; +7 Authors

    Abstract The effect of magnetic field ripple on tokamak plasma without turbulence is studied numerically and augmented with a reduced analytical model that includes neoclassical processes in the presence of non-axisymmetric perturbation and stochastic transport. For this study, a magnetic field ripple perturbation has been implemented in the GYSELA gyrokinetic code. This implementation has been verified thanks to a test of toroidal angular momentum conservation. The GYSELA code was then successfully benchmarked against the NEO code, which solves the drift kinetic equation, and against the reduced model in the collisionality range ν ⋆ ∈ [0.05–0.5] for several amplitudes of the magnetic ripple. An observation, shared by the model, the NEO code and GYSELA simulations is that the thermal drive of the mean poloidal velocity—measured by the k V P coefficient—decreases sharply for large yet experimentally relevant magnetic ripple amplitudes, and may even change sign.

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    Plasma Physics and Controlled Fusion
    Article . 2023 . Peer-reviewed
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      Plasma Physics and Controlled Fusion
      Article . 2023 . Peer-reviewed
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    Authors: Babak Rezaei; Jessica Giacomoni; Fredrik Nilsson; Edoardo Sozzi; +4 Authors

    Abstract Brain organoid technology has transformed both basic and applied biomedical research and paved the way for novel insights into developmental processes and disease states of the human brain. While the use of brain organoids has been rapidly growing in the past decade, the accompanying bioengineering and biofabrication solutions have remained scarce. As a result, most brain organoid protocols still rely on commercially available tools and culturing platforms that had previously been established for different purposes, thus entailing suboptimal culturing conditions and excessive use of plasticware. To address these issues, we developed a 3D printing pipeline for the fabrication of tailor-made culturing platforms for fluidically connected but spatially separated brain organoid array culture. This all-in-one platform allows all culturing steps—from cellular aggregation, spheroid growth, hydrogel embedding, and organoid maturation—to be performed in a single well plate without the need for organoid manipulation or transfer. Importantly, the approach relies on accessible materials and widely available 3D printing equipment. Furthermore, the developed design principles are modular and highly customizable. As such, we believe that the presented technology can be easily adapted by other research groups and fuel further development of culturing tools and platforms for brain organoids and other 3D cellular systems.

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    Biofabrication
    Article . 2023 . Peer-reviewed
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    Biofabrication
    Article . 2023
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