SMART-Morph

SMART-Morph: Smart Modules for AI-supported Serial X-Ray Micro Computed Tomography for Comparative Morphological Studies at PETRA III/IV

Objective & Goals

The ultimate goal is to create a highly efficient, automated, and quality-assured imaging process that benefits diverse scientific fields. By enabling large-scale studies with unprecedented detail, the project will enable the advancement of our understanding of genetic and environmental influences on morphology, support biodiversity research, and contribute to medical and ecological solutions.
Under its broader scope, the project includes developing robust and efficient algorithms, incorporating automation tools & techniques, leveraging robotics and AI to automate workflows for sample preparation, data acquisition, and analysis. This innovation enhances the capabilities of synchrotron facilities like PETRA III/IV, enabling large-scale digitization and precise morphological comparisons across thousands of biological samples. The project seeks to establish SµCT as a robust tool for life sciences, bridging morphology with molecular and ecological data to address key questions in developmental biology, biomedicine, ecology, and functional morphology.
The overall scheme of the envisioned imaging platform. The components include
instrumentation, including robotics, data flows (marked by arrows),and feedback
loops (marked by dashed arrows).

 

Areas of Research

  • Development of New Methodologies for synchrotron facilities: Creating robotic workflows and AI-assisted control systems to automate and enhance µCT scanning, data acquisition, and analysis for large sample series at photon facilities like PETRA III/IV
  • Broad Scientific Applications: Covering areas such as developmental biology, biomedicine, ecology, and functional morphology, with applications including studying biodiversity, disease models, and genetic influences on morphology.
  • Technological Advances: Developing automated sample preparation, intelligent control for experiments, and real-time data processing systems to handle vast data from large-scale studies.
  • Outreach and Education: Supporting public and academic dissemination through publications, museum exhibitions, and incorporation into educational resources.

Project Team from KIT-IPS and KIT-LAS

  • Dr. Tomáš Faragó
  • Dr. Marcus Zuber
  • Dr. Elias Hamann
  • Dr. Clément Tavakoli
  • Dr. Nikolay Zagainov
  • Chandan Sarkar
  • Janes Odar

In Collaboration With

Main Proposers:

  • Prof. Dr. Lars Krogmann (University of Hohenheim)
  • Prof. Dr. Joachim Wittbrodt and team (University of Heidelberg)
  • Prof. Dr. Tilo Baumbach and team (Karlsruhe Institute of Technology, LAS)
  • Prof. Dr.-Ing. Dr. h.c. Jürgen Becker (Karlsruhe Institute of Technology, ITIV)

Lead Participating Institutions

  • Karlsruhe Institute of Technology (KIT): Multiple departments for robotics, data processing, and synchrotron radiation applications
  • Centre for Organismal Studies (COS), Universität Heidelberg (UHEI)
  • KomBioTa - Kompetenzzentrum Biodiversität und integrative Taxonomie, Universität Hohenheim (UHOH)

Associated Project Partners:

  • Dr. Suren Chilingaryan, Dr. Andreas Kopmann Institut für Prozessdatenverarbeitung und Elektronik (IPE)
  • Dr. Thomas R. Schneider, Dr. Elizabeth Duke EMBL European Molecular Biology Laboratory, Hamburg
  • Dr. Dmitri Novikov, Dr. Carlos Sato Baraldi Dias P23 Team at Deutsches Elektronen-Synchrotron DESY
  • Dr. Julian Moosmann - Helmholtz-Zentrum Hereon; Geesthacht
  • Dr. Thomas van de Kamp, Dr. Tomáš Faragó, Dr. Elias Hamann Institut für Photonenforschung und Synchrotronstrahlung (IPS)
  • Dr. Hossein Rajaei Department of Entomology State Museum of Natural History Stuttgart (SMNS)

Other Partners:

  • Deutsches Elektronen-Synchrotron (DESY) for synchrotron facilities.
  • Natural history museums for biodiversity studies and sample provision.

Funding

SMART-Morph project is funded by the German Federal Ministry for Education and Research (BMBF) under the funding code 05K22VKA.