Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D

Ravian L van Ineveld, Michiel Kleinnijenhuis, Maria Alieva, Sam de Blank, Mario Barrera Roman, Esmée J van Vliet, Clara Martínez Mir, Hannah R Johnson, Frank L Bos, Raimond Heukers, Susana M Chuva de Sousa Lopes, Jarno Drost, Johanna F Dekkers, Ellen J Wehrens, Anne C Rios

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


Despite advances in three-dimensional (3D) imaging, it remains challenging to profile all the cells within a large 3D tissue, including the morphology and organization of the many cell types present. Here, we introduce eight-color, multispectral, large-scale single-cell resolution 3D (mLSR-3D) imaging and image analysis software for the parallelized, deep learning-based segmentation of large numbers of single cells in tissues, called segmentation analysis by parallelization of 3D datasets (STAPL-3D). Applying the method to pediatric Wilms tumor, we extract molecular, spatial and morphological features of millions of cells and reconstruct the tumor's spatio-phenotypic patterning. In situ population profiling and pseudotime ordering reveals a highly disorganized spatial pattern in Wilms tumor compared to healthy fetal kidney, yet cellular profiles closely resembling human fetal kidney cells could be observed. In addition, we identify previously unreported tumor-specific populations, uniquely characterized by their spatial embedding or morphological attributes. Our results demonstrate the use of combining mLSR-3D and STAPL-3D to generate a comprehensive cellular map of human tumors.

Original languageEnglish
Pages (from-to)1239-1245
Number of pages7
JournalNature biotechnology
Issue number10
Publication statusPublished - Oct 2021


  • Biomarkers, Tumor/metabolism
  • Deep Learning
  • Fluorescent Dyes
  • Humans
  • Image Processing, Computer-Assisted/methods
  • Imaging, Three-Dimensional/methods
  • Kidney/diagnostic imaging
  • Neoplasms/diagnostic imaging
  • Phenotype
  • Software


Dive into the research topics of 'Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D'. Together they form a unique fingerprint.

Cite this