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The Microscopy center puts collaboration first: its full range of instrumentation, technical support staff, and image analysis tools are there to remove all barriers to the Stowers Institute’s research scientists when it comes to electron or light microscopy.

The Microscopy Center is hiring!

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Overview of Services

Research Services

The Stowers Microscopy Center helps advance research at the institute by collaborating with lab members on scientific projects, maintaining a wide variety of microscopes both in the center and throughout the institute, and adapting or developing new technologies in anticipation of future imaging needs. The facility’s resources include electron microscopy, light microscopy, and computational resources. Our multidisciplinary team of physicists, software specialists, chemists, and biologists accelerate the pace of research with experimental design, execution, and analysis.


  • Zeiss Merlin SEM with Gatan 3View
  • FEI Talos F200C TEM
  • FEI Tecnai 120kV TEM
  • Hitachi TM4000 SEM
  • Zeiss Elyra 7 with Lattice SIM
  • Leica SP8 STED with Falcon Lifetime
  • Zeiss LSM 780 with AiryScan and OPO
  • 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
  • PerkinElmer Opera Phenix
  • Olympus VS120 Slide Scanner
  • Zeiss LSM 800
  • Zeiss LSM 700
  • Zeiss PALM Microbeam dissection microscope
  • EM labeling techniques: Immuno-gold and APEX2
  • 3D EM imaging: 3View, ATUMtome, tomography, 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)
  • Micro-fabrication and macro imaging

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Software & Computing

  • Fiji, IMOD, Imaris, Amira, Blender, napari, and various python libraries
  • Deep learning using DeepFiji and Tensorflow
  • 10 High performance workstations
  • 2 Workstations with Deep Learning GPUs

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Team Contact

Sean McKinney

Director, Microscopy

Stowers Institute for Medical Research

Portrait of Sean McKinney
Portrait of Amanda Kroesen

Amanda Kroesen

Associate Scientist

Portrait of Jeff Lange

Jeff Lange


Portrait of Cindy Maddera

Cindy Maddera

Associate Scientist

Portrait of Melania McClain

Melania McClain


Portrait of Cathy McKinney

Cathy McKinney


Portrait of Jason Morrison

Jason Morrison


Portrait of Steph Nowotarski

Steph Nowotarski


Portrait of Chris Wood

Chris Wood


Portrait of Kexi Yi

Kexi Yi

Manager, Electron Microscopy

Portrait of Zulin Yu

Zulin Yu

Manager, Light Microscopy

Portrait of Xia Zhou

Xia Zhao

Associate Scientist

Our Microscopy Suite

Seeing is believing – being able to find, track, or examine interactions is more important than ever. Our extensive array of microscopes allow Stowers researchers to tease apart details from samples of all sizes: from the molecular level up to whole animals.


With the Zeiss Elyra 7 Lattice SIM, 60 nm optical resolution is achievable, extending sub-organelle or meiotic DNA structure imaging to up to 80 mm deep. For smaller samples the Leica SP8 STED can push the resolution limits even further to 40nm or better.

PerkinElmer Opera Phenix

High-speed imaging

The center automates the imaging of organisms from whole animals down to single cells for hundreds or thousands of samples with a robot-equipped Nikon spinning disk and a Perkin Elmer Opera Phenix.

Zeiss LSM 780

Multiplex and FRET Imaging

More colors equals more information. Using the Zeiss LSM 780 or the Leica SP8 with Falcon Lifetime we can separate up to 8 colors from one another, expanding researchers’ options for finding just the right target. With fluorescence lifetime imaging, looking at protein interactions with FRET is a snapshot away.

3-Dimensional Electron Microscopy

SEM imaging and reconstructing serial sections becomes routine with the Zeiss Merlin SEM. The 3View upgrade by Gatan does away with cutting artifacts by imaging the surface of the block face and cutting afterwards.

Talos 200C Transmission Electron Microscope

Ultimate Resolution

The new Talos 200C Transmission Electron Microscope gives resolution limited only by one’s ability to preserve a sample’s ultrastructure. The software and high beam energy allow users to acquire 3D tomography data in thicker sections for the first time. The accompanying cryo holder allows for screening of grids for single particle averaging analysis.


Software has become as crucial to the enterprise of microscopy as confocal and electron microscopes. This is demanded by the advanced quantitation required in modern biology and by the sheer quantity of data acquired. Much of the ImageJ software we develop is publicly available at Please follow the instructions there to follow our Stowers Fiji update site. Published source code is available on our individual GitHub sites. Here are the links to those sites:

Sean McKinney:

Chris Wood:

Richard Alexander:

Sarah Smith:

Jay Unruh:

Featured Publications

wtf4 meiotic driver utilizes controlled protein aggregation to generate selective cell death

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.

Wnt and TGF-β coordinate growth and patterning to regulate size-dependent behavior

Arnold CP, Benham-Pyle BW, Lange JJ, Wood CJ, Sánchez Alvarado A. Nature. 2019;572:655-659.

Yeast centrosome components form a noncanonical LINC complex at the nuclear envelope insertion site.

Chen J, Gardner JM, Yu Z, Smith SE, McKinney S, Slaughter BD, Unruh JR, Jaspersen SL.  J Cell Biol. 2019;218:1478-1490.

The E3 ubiquitin ligase SINA regulates the assembly and disassembly of the synaptonemal complex in Drosophila females

Hughes SE, Hemenway E, Guo F, Yi K, Yu Z, Hawley RS. PLoS Genet. 2019;15:e1008161. doi: 10.1371/journal.pgen.1008161.

Prospectively Isolated Tetraspanin(+) Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration

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.

An axial Hox code controls axial patterning and tissue segmentation in Nematostella vectensis

He S, Del Viso F, Chen CY, Ikmi A, Kroesen AE, Gibson MC. Science. 2018;361:1377-1380.

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