Automatic Stem Cell Detection in Microscopic Whole Mouse Cryo-Imaging

Patiwet Wuttisarnwattana, Madhusudhana Gargesha, Wouter Van'T Hof, Kenneth R. Cooke, David L. Wilson

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


With its single cell sensitivity over volumes as large as or larger than a mouse, cryo-imaging enables imaging of stem cell biodistribution, homing, engraftment, and molecular mechanisms. We developed and evaluated a highly automated software tool to detect fluorescently labeled stem cells within very large (∼ 200 GB) cryo-imaging datasets. Cell detection steps are: preprocess, remove immaterial regions, spatially filter to create features, identify candidate pixels, classify pixels using bagging decision trees, segment cell patches, and perform 3D labeling. There are options for analysis and visualization. To train the classifier, we created synthetic images by placing realistic digital cell models onto cryo-images of control mice devoid of cells. Very good cell detection results were (precision = 98.49%, recall = 99.97%) for synthetic cryo-images, (precision = 97.81%, recall = 97.71%) for manually evaluated, actual cryo-images, and < 1% false positives in control mice. An α-multiplier applied to features allows one to correct for experimental variations in cell brightness due to labeling. On dim cells (37% of standard brightness), with correction, we improved recall (49.26% → 99.36%) without a significant drop in precision (99.99% → 99.75%). With tail vein injection, multipotent adult progenitor cells in a graft-versus-host-disease model in the first days post injection were predominantly found in lung, liver, spleen, and bone marrow. Distribution was not simply related to blood flow. The lung contained clusters of cells while other tissues contained single cells. Our methods provided stem cell distribution anywhere in mouse with single cell sensitivity. Methods should provide a rational means of evaluating dosing, delivery methods, cell enhancements, and mechanisms for therapeutic cells.

Original languageEnglish (US)
Article number7315046
Pages (from-to)819-829
Number of pages11
JournalIEEE transactions on medical imaging
Issue number3
StatePublished - Mar 2016


  • Biodistribution
  • Visualization
  • cell
  • cell detection
  • cryo-imaging
  • fluorescent imaging
  • image processing
  • machine learning
  • optical imaging
  • segmentation
  • stem cell homing

ASJC Scopus subject areas

  • Software
  • Radiological and Ultrasound Technology
  • Computer Science Applications
  • Electrical and Electronic Engineering


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