The Microscopy team offers a full range of instrumentation, technical support, and collaborative services to Stowers scientists whose research involves optical or electron microscopy.

Research Services 

The Stowers Microscopy Center enables research at Stowers by collaborating scientifically on projects, maintaining a wide variety of microscopes throughout the Institute, and developing new technologies in anticipation of future microscopic needs. The facility’s resources include electron microscopy, light microscopy, and computational resources. With a large staff of physicists, software specialists, chemists, and biologists, the team is capable of experimental design, execution, and analysis, thus accelerating the pace of experimentation.



  • Zeiss Merlin SEM with Gatan 3View
  • FEI Technai Spirit BioTwin 120kV TEM
  • Hitachi TM4000 SEM
  • Leica EM PACT
  • Leica FC6 cryoattachment
  • PELCO BioWave Laboratory Processing Robot
  • Zeiss LSM 780 with AiryScan and OPO
  • Leica SP8 STED
  • DeltaVision OMX
  • Nikon Ti Eclipse with CSU-W1 Spinning Disk and PLW20 Well Plate Loader
  • Nikon Ti2 with CSU-W1 Spinning Disk and Opti Microscan FRAP Unit
  • Olympus VS120 Slide Scanner
  • Zeiss LSM 710 with 2PE
  • Zeiss LSM 700 Inverted
  • Zeiss LSM 700 Upright
  • Zeiss PALM Microbeam dissection microscope

Special methods:

  • EM labeling techniques:  Immuno-gold and APEX2
  • 3D EM imaging:  3view, ATUMtome, and traditional serial sectioning
  • Super-resolution techniques:  SIM, STED, PALM, STORM
  • Protein interaction techniques:  FRET, FRAP, FCS, FCCS
  • Robotic imaging platforms and software for automated imaging
  • Laser microdissection, ablation, and heat stimulation
  • Selective Plane Illumination Microscopy (SPIM)


  • Fiji, IMOD, Imaris, Amira and various python libraries
  • Deep learning using DeepFiji and Tensorflow
  • 10 High performance workstations
  • 2 Workstations with Deep Learning GPUs
Team Contact 
Sean McKinney, PhD
Director, Microscopy

After graduating from the University of Missouri, Rolla with a BS in Physics and Computer Science, Sean McKinney earned his PhD studying DNA conformations at the single molecule level using fluorescence resonance energy transfer (FRET) at the University of Illinois, Urbana-Champaign. He was a Research Specialist at the Janelia Farm Research Campus before joining the Stowers Microscopy team in 2009 as the group head of Optics Development. He was named manager of Microscopy in 2015, and in 2019 he was appointed head of Microscopy. McKinney and his team automate imaging with robotics and image analysis through deep learning which allows researchers to perform customized large-scale imaging screens.

Featured Publications 
Nuckolls NL, Mok AC, Lange JJ, Yi K, Kandola TS, Hunn AM, McCroskey S, Snyder JL, Bravo Nunez MA, McClain M, McKinney SA, Wood C, Halfmann R, Zanders SE.  eLife. 2020;9:e55694. doi: 55610.57554/eLife.55694.
Arnold CP, Benham-Pyle BW, Lange JJ, Wood CJ, Sánchez Alvarado A. Nature. 2019;572:655-659.
Chen J, Gardner JM, Yu Z, Smith SE, McKinney S, Slaughter BD, Unruh JR, Jaspersen SL.  J Cell Biol. 2019;218:1478-1490.
Hughes SE, Hemenway E, Guo F, Yi K, Yu Z, Hawley RS. PLoS Genet. 2019;15:e1008161. doi: 10.1371/journal.pgen.1008161.
Zeng A, Li H, Guo L, Gao X, McKinney S, Wang Y, Yu Z, Park J, Semerad C, Ross E, Cheng LC, Davies E, Lei K, Wang W, Perera A, Hall K, Peak A, Box A, Sánchez Alvarado A. Cell. 2018;173:1593-1608.e20.
He S, Del Viso F, Chen CY, Ikmi A, Kroesen AE, Gibson MC. Science. 2018;361:1377-1380.
Kozlovskaja-Gumbriene A, Yi R, Alexander R, Aman A, Jiskra R, Nagelberg D, Knaut H, McClain M, Piotrowski T. eLife. 2017;6: e21049. doi: 21010.27554/eLife.21049.
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