Developing the eHistology Atlas

Abstract

The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook 'The Atlas of Mouse Development' by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php.

Figure 1.

eHistology Atlas IIP3D Viewer Details. This figure shows the various options and navigation tools available within the IIP3D viewer used in the eHistology Atlas. Plate 25b (image a) is shown, with the colour section image displayed in the central panel at 1:8 magnification, the anatomy labels are listed on the right, and navigation tools shown on the left. Clicking on a numbered flag opens up the floating pop-up window containing internal and external links. Image is provided with permission from eMouseAtlas.

Figure 2.

eHistology Atlas plate/stage browser. This figure shows the various elements of the eHistology Atlas plate/stage browser. Users are presented with this browser when they access the eHistology Atlas. They are able to scroll through the plates using the filmstrip browser at the top of the page. By selecting any particular plate, the user will then see the central panel in the browser alter to reflect the contents of the chosen plate. A larger version of the embryo schematic is shown on the left, with all of the section planes delineated to show the approximate position within the embryo, of each section. One section position is highlighted in red, and the relevant section image for this position is shown on the right. The user is able to change the selected section using the section filmstrip at the bottom of the page. The central panel displays the metadata for each selected plate. Having chosen a section of interest the user then launches the IIP3D viewer using the button in the central panel. Image is provided with permission from eMouseAtlas.