Scientific studies of 3D morphology over a very large number of shapes face a challenge of viewing and comparing thousands of shapes. The goal of our work is to create a web application that can support visual inspections in a browser to enable collaborative discoveries.
This work is motivated by a biological study about stem cell and scaffold interactions. To derive significant conclusions about these cells, biologists must be able to view and study a large number of 3D images rapidly. The problem addressed is to design a web application that enables viewing high numbers of 3D data sets interactively while managing memory usage.
Figure 1 illustrates a typical visual inspection sequence that involves changing spatial resolutions and the number of cells being scrutinized. The interactive system is available at the URL.
We approached the problem by creating the Mass Stem Cell 3D Web Viewer, which is comprised of two components:
The Viewer supports scientists with the following features:
Selecting cells from multiple scaffolds Translating, rotating and zooming Color-coding and sorting based on file name, volume, surface, depth, and three principal axes lengths Tooltip display with scaffold, file name and pyramid resolution for each cell Downloading a csv file with all 3D shape properties Help and instructions
We have prototyped a web solution that enables viewing 1147 cells acquired on 10 different scaffolds (approximately 110 cells per scaffold, 122,949 images and 122 GB of data). The Viewer runs on client computers with minimal RAM specifications. The key contributions of our work lie in:
Enabling scalable transmission and viewing of thousands of 3D data sets Providing interactive visual inspection functions Analyzing the Viewer’s client-side RAM and server-side disk storage requirements