What is Optical projection tomography (OPT)?

Optical projection tomography (OPT) is the technique used to generate the 3D models in the ZFAP resource.

The process of Optical Projection Tomography (OPT) was described by Sharpe et al. (2002). The application of OPT to zebrafish is described in Bryson-Richardson and Currie (Bryson-Richardson and Currie 2004).

To generate 3D images in OPT a series of images is captured of the sample as it rotates. Each line of pixels in these images is then back projected to generate a cross section through the sample. The process of back projection is illustrated in Figure 1.

By joining the back projected images from every line of pixels a complete 3D model is generated.

principle of OPT
Figure 1

scan of 7mm sample
Figure 2

The 3D models in ZFAP were generated by imaging the autofluorescence of paraformaldehyde fixed zebrafish. Samples were bleached using hydrogen peroxide to remove pigmentation and cleared using benzyl alcohol:benzyl benzoate.

Figure 2 shows a scan of a 7mm long zebrafish specimen.

Similarly to the example in Figure 1 these projection images can be used to generate a cross section through the sample (Figure 3).

Once the cross sections have been generated and used to generate a 3D model. The model can be virtually cut to generate sections in other planes, such as those in ZFAP.

Demonstration of a reconstruction to form a cross section image
Figure 3


Bryson-Richardson RJ, Currie PD. Optical projection tomography for spatio-temporal analysis in the zebrafish.

Methods Cell Biol. 2004;76:37-50

Sharpe J, Ahlgren U, Perry P, Hill B, Ross A, Hecksher-Sorensen J, Baldock R, Davidson D. Optical projection tomography as a tool for 3D microscopy and gene expression studies.

Science. 2002 Apr 19;296(5567):541-5.