---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21231'
abstract:
- lang: eng
  text: To assess cell migration in complex spatial environments, microfabricated
    chips, such as mazes and pillar forests, are routinely used to impose spatial
    and mechanical constraints, and cell trajectories are followed within these structures
    by advanced imaging techniques. In systems mechanobiology, computational models
    serve as essential tools to uncover how physical geometry influences intracellular
    dynamics; however, decoding such complex behaviors requires advanced inference
    techniques. Here, we integrated experimental observations of dendritic cell migration
    in a geometrically constrained microenvironment into a Cellular Potts model. We
    demonstrated that these spatial constraints modulate the motility dynamics, including
    speed and directional changes. We show that classical summary statistics, such
    as mean squared displacement and turning angle distributions, can resolve key
    mechanistic features but fail to extract richer spatiotemporal patterns, limiting
    accurate parameter inference. To solve this, we applied neural posterior estimation
    with in-the-loop learning of summary features. This learned summary representation
    of the data enables robust and flexible parameter inference, providing a data-driven
    framework for model calibration and advancing quantitative analysis of cell migration
    in structured microenvironments.
acknowledgement: 'This work was supported by the German Federal Ministry of Education
  and Research (BMBF) (EMUNE/031L0293C), the European Union via the ERC grant INTEGRATE,
  grant agreement number 101126146, and under Germany’s Excellence Strategy by the
  Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (EXC 2047—390685813,
  EXC 2151—390873048, FOR5775 — 533863915, and 524747443), the University of Bonn
  via the Schlegel Professorship of J.H., and the returning experts fellowship of
  the Ministry of Innovation, Science, and Research of North-Rhine-Westphalia (AZ:
  421-8.03.03.02-137069). J.M. is a member of the Nanofabrication Facility and is
  supported by the Institute of Science and Technology Austria. E.K. acknowledges
  the TRA Life and Health (University of Bonn) as part of the Excellence Strategy
  of the federal and state governments. The authors thank Laeschkir Würthner for his
  insightful comments on the implementation of the authors’ model. The views and opinions
  expressed are those of the authors only and do not necessarily reflect those of
  the funding agencies. Parts of Fig. 1 were created using BioRender. Open Access
  funding enabled and organized by Projekt DEAL.'
article_number: '20'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jonas
  full_name: Arruda, Jonas
  last_name: Arruda
- first_name: Emad
  full_name: Alamoudi, Emad
  last_name: Alamoudi
- first_name: Robert
  full_name: Mueller, Robert
  last_name: Mueller
- first_name: Marc
  full_name: Vaisband, Marc
  last_name: Vaisband
- first_name: Ronja
  full_name: Molkenbur, Ronja
  last_name: Molkenbur
- first_name: Jack
  full_name: Merrin, Jack
  id: 4515C308-F248-11E8-B48F-1D18A9856A87
  last_name: Merrin
  orcid: 0000-0001-5145-4609
- first_name: Eva
  full_name: Kiermaier, Eva
  last_name: Kiermaier
- first_name: Jan
  full_name: Hasenauer, Jan
  last_name: Hasenauer
citation:
  ama: Arruda J, Alamoudi E, Mueller R, et al. Simulation-based inference of cell
    migration dynamics in complex spatial environments. <i>npj Systems Biology and
    Applications</i>. 2026;12. doi:<a href="https://doi.org/10.1038/s41540-026-00648-9">10.1038/s41540-026-00648-9</a>
  apa: Arruda, J., Alamoudi, E., Mueller, R., Vaisband, M., Molkenbur, R., Merrin,
    J., … Hasenauer, J. (2026). Simulation-based inference of cell migration dynamics
    in complex spatial environments. <i>Npj Systems Biology and Applications</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41540-026-00648-9">https://doi.org/10.1038/s41540-026-00648-9</a>
  chicago: Arruda, Jonas, Emad Alamoudi, Robert Mueller, Marc Vaisband, Ronja Molkenbur,
    Jack Merrin, Eva Kiermaier, and Jan Hasenauer. “Simulation-Based Inference of
    Cell Migration Dynamics in Complex Spatial Environments.” <i>Npj Systems Biology
    and Applications</i>. Springer Nature, 2026. <a href="https://doi.org/10.1038/s41540-026-00648-9">https://doi.org/10.1038/s41540-026-00648-9</a>.
  ieee: J. Arruda <i>et al.</i>, “Simulation-based inference of cell migration dynamics
    in complex spatial environments,” <i>npj Systems Biology and Applications</i>,
    vol. 12. Springer Nature, 2026.
  ista: Arruda J, Alamoudi E, Mueller R, Vaisband M, Molkenbur R, Merrin J, Kiermaier
    E, Hasenauer J. 2026. Simulation-based inference of cell migration dynamics in
    complex spatial environments. npj Systems Biology and Applications. 12, 20.
  mla: Arruda, Jonas, et al. “Simulation-Based Inference of Cell Migration Dynamics
    in Complex Spatial Environments.” <i>Npj Systems Biology and Applications</i>,
    vol. 12, 20, Springer Nature, 2026, doi:<a href="https://doi.org/10.1038/s41540-026-00648-9">10.1038/s41540-026-00648-9</a>.
  short: J. Arruda, E. Alamoudi, R. Mueller, M. Vaisband, R. Molkenbur, J. Merrin,
    E. Kiermaier, J. Hasenauer, Npj Systems Biology and Applications 12 (2026).
date_created: 2026-02-16T10:44:31Z
date_published: 2026-02-05T00:00:00Z
date_updated: 2026-02-23T10:10:10Z
day: '05'
ddc:
- '570'
department:
- _id: NanoFab
doi: 10.1038/s41540-026-00648-9
external_id:
  pmid:
  - '41611727'
file:
- access_level: open_access
  checksum: 99b2e6bbaaedf45f22e07751948669f5
  content_type: application/pdf
  creator: dernst
  date_created: 2026-02-23T10:09:03Z
  date_updated: 2026-02-23T10:09:03Z
  file_id: '21346'
  file_name: 2026_npjSysBioApp_Arruda.pdf
  file_size: 10217687
  relation: main_file
  success: 1
file_date_updated: 2026-02-23T10:09:03Z
has_accepted_license: '1'
intvolume: '        12'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: npj Systems Biology and Applications
publication_identifier:
  eissn:
  - 2056-7189
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simulation-based inference of cell migration dynamics in complex spatial environments
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2026'
...