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Whole-mount three-dimensional imaging of internally localized immunostained cells within mouse embryos

Nature Protocols volume 7, pages 421431 (2012) | Download Citation


We describe a three-dimensional (3D) confocal imaging technique to characterize and enumerate rare, newly emerging hematopoietic cells located within the vasculature of whole-mount preparations of mouse embryos. However, the methodology is broadly applicable for examining the development and 3D architecture of other tissues. Previously, direct whole-mount imaging has been limited to external tissue layers owing to poor laser penetration of dense, opaque tissue. Our whole-embryo imaging method enables detailed quantitative and qualitative analysis of cells within the dorsal aorta of embryonic day (E) 10.5–11.5 embryos after the removal of only the head and body walls. In this protocol we describe the whole-mount fixation and multimarker staining procedure, the tissue transparency treatment, microscopy and the analysis of resulting images. A typical two-color staining experiment can be performed and analyzed in 6 d.

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We thank the members of the laboratory for critical comments related to this work and also thank the following funding organizations: the US National Institutes of Health grants R37DK054077 (E.D.) and RO1HL091724 (N.A.S.), the Netherlands BSIK Innovation Program 03040 (E.D.) and the European Science Foundation Program EuroSTELLS 01-011 (E.D.), and the Netherlands Genomics Initiative—Cancer Genomic Distinguished Scientist Award (N.A.S.).

Author information


  1. Department of Cell Biology, Erasmus Medical Center Stem Cell Institute, Erasmus Medical Center, Rotterdam, The Netherlands.

    • Tomomasa Yokomizo
    • , Tomoko Yamada-Inagawa
    •  & Elaine Dzierzak
  2. Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.

    • Tomomasa Yokomizo
  3. Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Amanda D Yzaguirre
    • , Michael J Chen
    •  & Nancy A Speck


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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Tomomasa Yokomizo.

Supplementary information


  1. 1.

    Supplementary Video 1

    3D reconstructed video of a whole E9 embryo (14 sp). Ly6A-GFP transgenic embryo was stained with anti-GFP antibody (green) and anti-CD31 antibody (magenta). Picture was taken by x10 objective (HC PL APO CS x10/NA 0.4). Video was generated by Bitplane Imaris (Bitplane AG, Zurich Switzerland) assembling 311 slices (optical sections with 1.3 µm per z-step).

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