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Preprint

3D reconstruction of SGs

SC SeYeon Chung
DA Deborah J Andrew

Last updated date: Jul 1, 2020 Views: 954 Forks: 0

original An abbreviated version of this protocol was published in eLife in Mar, 2017
Uncoupling apical constriction from tissue invagination
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All confocal images that were used in the paper were taken with a Zeiss LSM 780 microscope, using 63x objective and 1.6x zoom (1024x1024). Each Z section was 0.37 um apart and each image consists of 20-40 z sections.


  1. Open a confocal image in Imaris.

  2. Create a new Surface.

  3. Choose "Skip automatic creation, edit manually".

  4. Choose "Source Channel" (e.g., Channel 1 - Green).

  5. Choose "Smooth Detail" – for most of the images in the paper, 0.165 um was used.

  6. Choose "Thresholding" – for most of the images in the paper, "Absolute Intensity" was used and manually adjusted.

  7. Filter using "Number of Voxels" if needed.

  8. Finish all creation steps.

  9. Return to step 2 for the next channel if needed.

  10. Choose different colors for each surface created if needed.

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Chung, S and Andrew, D(2020). 3D reconstruction of SGs. Bio-protocol Preprint. bio-protocol.org/prep358.
  2. Chung, S., Kim, S. and Andrew, D. J.(2017). Uncoupling apical constriction from tissue invagination. eLife. DOI: 10.7554/eLife.22235

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