Protocols

Summary

These pages provide details about the processes used to create 3D volumetric models from mouse embryos.

The processes have been divided into 5 sections, Embryo Collection, OPT scanning, Histology, Image Capture and Image Processing. Protocols are described for each of these sections.

The protocols have also varied over the life of the e-Mouse Atlas project as described in Protocol History. These protocol variants are described separately in each section.

1. Embryo Collection - embryos are collected and prepared for histological sectioning or OPT.
1. Epoxy resin.
2. Wax (Kaufman book).
3. Agarose for OPT.
4. Acrylic resin.
5. Epoxy resin TAAB PREMIX.
2. OPT scanning - embryos are scanned using Optical Projection Tomography.
3. Histology - embryos are sectioned and prepared on slides.
1. Epoxy resin.
2. Wax (Kaufman book).
3. Wax post OPT.
4. Acrylic resin.
5. Epoxy resin TAAB PREMIX.
4. Image Capture - slides are captured as digital images using a microscope and digital camera.
1. Configuration A.
2. Configuration B.
3. Configuration C.
4. Configuration D.
5. Configuration E.
5. Image Processing - digital images are aligned and stacked to form a 3D volume.
1. Method 1.
2. Method 2.
3. Method 3.
4. Method 4.

There is also a further section regarding protocols for movie production

• Movies Protocols

Protocol History

The protocols have varied over the lifetime of the project.

The development of OPT scanning has allowed a significant improvement in the digital recontruction of the models, as it is used as a scaffold that retains the shape of the embryo, so that the histology sections can be aligned more accurately.

A summary of the protocol variants