JAtlasViewer

JAtlasViewer is a program for selecting and viewing virtual sections from woolz format 3D images. Since any arbitrary section plane can be chosen, it can be used to explore the internal space of these 3D images.

Examples of suitable format 3D images include the EMAP mouse embryo models, the EADHB human embryo models and 3D images of gene expression patterns that have been generated using Optical Projection Tomography and are housed in the EMAGE database.
In some of the EMAP and EADHB models, anatomical regions are delineated in 3D and these too can be visualised with respect to each other and the entire organism using JAtlasViewer.

Start JAtlasViewer

Sample 3D woolz data sets for download:

Data Set Installation:

Depending upon which file you down-loaded you can install the sample data-set using:

  • unzip cs17.zip
    OR
  • gtar zxf cs17.tar.gz

Microsoft Windows users may prefer to use Winzip.

The down-loaded file will unpack to a folder calledcs17 which contains:

  • anatomy (folder containing anatomy components)
  • cs17.vtk (the 3D surface representing the cs17 embryo)
  • cs17.wlz (the 3D reconstruction of the cs17 embryo)

Screenshots:

cs17

 

 

This work has been partially funded by the NIH HBP grant "Electronic Atlas of the Human Embryonic Brain Gene Expression" in order to view digital reconstructions of human and mouse embryos at different stages of development.