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

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

StageModel IDEmbryo CollectionOPT scanHistologyImage CaptureImage Processing
TS01      
TS02      
TS03      
TS04      
TS05      
TS06      
TS07 EMA:7Epoxy resin NoEpoxy resinConfiguration AMethod1
TS08 EMA:8Epoxy resinNoEpoxy resinConfiguration AMethod1
TS09 EMA:9Epoxy resin NoEpoxy resinConfiguration AMethod1
TS10 EMA:10Epoxy resin NoEpoxy resinConfiguration AMethod1
TS11 EMA:17Epoxy resin NoEpoxy resinConfiguration AMethod1
TS12 EMA:21Epoxy resin NoEpoxy resinConfiguration AMethod1
TS12 EMA:145Epoxy resin TAAB YesEpoxy resin TAABConfiguration D Method4
TS13 EMA:24Wax (Kaufman book)NoWax (Kaufman book)Configuration AMethod1
TS14 EMA:27Wax (Kaufman book)No Wax (Kaufman book)Configuration AMethod1
TS15 EMA:36Agarose for OPTYesWax post OPTConfiguration CMethod3
TS16 EMA:47Agarose for OPTYesWax post OPTConfiguration BMethod3
TS17 EMA:52Agarose for OPTYesWax post OPTConfiguration CMethod3
TS18 EMA:63Agarose for OPTYesWax post OPTConfiguration BMethod3
TS19 EMA:75Agarose for OPTYesWax post OPTConfiguration CMethod3
TS20 EMA:76Wax (Kaufman book)NoWax (Kaufman book)Configuration AMethod1
TS21 EMA:78Agarose for OPTYesWax post OPTConfiguration DMethod3
TS22 EMA:79Agarose for OPTYesWax post OPTConfiguration DMethod3
TS23 EMA:99Agarose for OPTYesWax post OPTConfiguration DMethod3
TS23 limb special system
EMA:108, EMA:109
Agarose for OPTYesWax post OPTConfiguration DMethod3
TS23kidney special system
EMA:105
Agarose for OPTYesWax post OPTConfiguration DMethod3
TS24 EMA:100Agarose for OPTYesWax post OPTConfiguration DMethod3
TS25 EMA:101Agarose for OPTYesWax post OPTConfiguration DMethod3
TS26 EMA:102Wax (Kaufman book)NoWax (Kaufman book)Configuration EMethod2
TS26kidney special system
EMA:103
Acrylic resinNoAcrylic resinConfiguration DMethod3
TS27      
TS28