Deconvolution Stepwise Optical Saturation (DeSOS) Microscopy Program



Super-resolution microscopy is broadening our in-depth understanding of cellular structure. However, super-resolution approaches are limited, for numerous reasons, from utilization in longer-term intravital imaging. We devised a combinatorial imaging technique that combines deconvolution with stepwise optical saturation microscopy (DeSOS) to circumvent this issue and image cells in their native physiological environment. Other than a traditional confocal or two-photon microscope, this approach requires no additional hardware. Here, we provide an open-access application to obtain DeSOS images from conventional microscope images obtained at low excitation powers. We show that DeSOS can be used in time-lapse imaging to generate super-resolution movies in zebrafish. DeSOS was also validated in live mice. These movies uncover that actin structures dynamically remodel to produce a single pioneer axon in a “top-down” scaffolding event. Further, we identify an F-actin population – stable base clusters – that orchestrate that scaffolding event. We then identify that activation of Rac1 in pioneer axons destabilizes stable base clusters and disrupts pioneer axon formation. The ease of acquisition and processing with this approach provides a universal technique for biologists to answer questions in living, intact animals.

For more details, please refer to our publication:

Yide Zhang, Evan L. Nichols, Abigail M. Zellmer, Ian H. Guldner, Cody Kankel, Siyuan Zhang, Scott S. Howard, and Cody J. Smith, “Generating intravital super-resolution movies with conventional microscopy reveals actin dynamics that construct pioneer axons”, Development, in press, Feb. 2019, doi: 10.1242/dev.171512. Supplementary software available at doi: 10.7274/r0-5hhg-5578.

Featured News

YouTube video showing the comparison between conventional and DeSOS microscopy images


Attribute NameValues
Document Type
  • Software

Alternate Title
  • Generating intravital super-resolution movies with conventional microscopy reveals actin dynamics that construct pioneer axons

  • Yide Zhang

  • Scott S. Howard

  • Cody J. Smith

  • Yide Zhang

  • Evan L. Nichols

  • Abigail M. Zellmer

  • Ian H. Guldner

  • Cody Kankel

  • Siyuan Zhang

  • Scott S. Howard

  • Cody J. Smith

Date Created
  • 2019-01-09

  • University of Notre Dame

  • Super-resolution microscopy

  • Biological sciences

  • Confocal microscopy

  • Two-photon microscopy

Contributor Institution
  • Department of Electrical Engineering, University of Notre Dame

  • Department of Biological Sciences, University of Notre Dame

  • Center for Stem Cells and Regenerative Medicine, University of Notre Dame

  • Mike and Josie Harper Cancer Research Institute, University of Notre Dame

  • Indiana University Melvin and Bren Simon Cancer Center

  • Center for Research Computing. University of Notre Dame

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Record Visibility Public
Content License
  • All rights reserved

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This DOI is the best way to cite this software.


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