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@ARTICLE{Kamboj:302015,
      author       = {O. Kamboj and J. Park and O. Stegle$^*$ and F. A.
                      Hamprecht},
      title        = {{F}rom spots to cells: {C}ell segmentation in spatial
                      transcriptomics with {BOMS}.},
      journal      = {PLOS ONE},
      volume       = {20},
      number       = {6},
      issn         = {1932-6203},
      address      = {San Francisco, California, US},
      publisher    = {PLOS},
      reportid     = {DKFZ-2025-01213},
      pages        = {e0311458 -},
      year         = {2025},
      abstract     = {Imaging-based Spatial Transcriptomics methods enable the
                      study of gene expression and regulation in complex tissues
                      at subcellular resolution. However, inaccurate cell
                      segmentation procedures lead to misassignment of mRNAs to
                      individual cells which can introduce errors in downstream
                      analysis. Current methods estimate cell boundaries using
                      auxiliary DAPI/Poly(A) stains. These stains can be difficult
                      to segment, thus requiring manual tuning of the method, and
                      not all mRNA molecules may be assigned to the correct cells.
                      We describe a new method, based on mean shift, that segments
                      the cells based on the spatial locations and the gene labels
                      of the mRNA spots without requiring any auxiliary images. We
                      evaluate the performance of BOMS across various publicly
                      available datasets and demonstrate that it achieves
                      comparable results to the best existing method while being
                      simple to implement and significantly faster in execution.
                      Open-source code is available at
                      https://github.com/sciai-lab/boms.},
      keywords     = {Transcriptome / Gene Expression Profiling: methods / RNA,
                      Messenger: genetics / RNA, Messenger: metabolism / Humans /
                      Software / Algorithms / Image Processing, Computer-Assisted:
                      methods / RNA, Messenger (NLM Chemicals)},
      cin          = {B260},
      ddc          = {610},
      cid          = {I:(DE-He78)B260-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40504785},
      doi          = {10.1371/journal.pone.0311458},
      url          = {https://inrepo02.dkfz.de/record/302015},
}