3-Dimensional Reconstruction From Histopathological Sections: A Systematic Review

Research output: Contribution to journalReview articleContributedpeer-review


  • Alexander Kurz - , German Cancer Research Center (DKFZ) (Author)
  • Heimo Müller - , Medical University of Graz (Author)
  • Jakob N. Kather - , Else Kröner Fresenius Center for Digital Health (Author)
  • Lucas Schneider - , German Cancer Research Center (DKFZ) (Author)
  • Tabea C. Bucher - , German Cancer Research Center (DKFZ) (Author)
  • Titus J. Brinker - , German Cancer Research Center (DKFZ) (Author)


Although pathological tissue analysis is typically performed on single 2-dimensional (2D) histologic reference slides, 3-dimensional (3D) reconstruction from a sequence of histologic sections could provide novel opportunities for spatial analysis of the extracted tissue. In this review, we analyze recent works published after 2018 and report information on the extracted tissue types, the section thickness, and the number of sections used for reconstruction. By analyzing the technological requirements for 3D reconstruction, we observe that software tools exist, both free and commercial, which include the functionality to perform 3D reconstruction from a sequence of histologic images. Through the analysis of the most recent works, we provide an overview of the workflows and tools that are currently used for 3D reconstruction from histologic sections and address points for future work, such as a missing common file format or computer-aided analysis of the reconstructed model.


Original languageEnglish
Article number102049
JournalLaboratory investigation
Issue number6
Early online date19 Mar 2024
Publication statusPublished - Jun 2024

External IDs

PubMed 38513977


ASJC Scopus subject areas


  • 3D reconstruction, histology, image alignment, image registration, whole slide image, Animals, Imaging, Three-Dimensional/methods, Humans, Software