Choi, Jinho (2013-08). Knife-Edge Scanning Microscope Mouse Brain Atlas In Vector Graphics For Enhanced Performance. Master's Thesis. Thesis uri icon

abstract

  • The microstructure of the brain at the cellular level provides crucial information for the understanding of the function of the brain. A large volume of high-resolution brain image data from 3D microscopy is an essential resource to study detailed microstructures of the brain. Accordingly, we have worked on obtaining high-resolution image data of entire mouse brains using the Knife-Edge Scanning Microscope (KESM). Furthermore, to disseminate these high-resolution whole mouse brain data sets to the neuroscience research community, we developed a web-based brain atlas, the KESM Brain Atlas (KESMBA). To visualize the data sets in 3D while using only a standard web browser, we employed distance attenuation and Google Maps API. The KESMBA is a powerful tool to analyze and share the KESM mouse brain data sets, but the image loading was slow because of the number of raster image (PNG) tiles and the file size. Moreover, since Google Maps API is governed by a commercial license, it does not provide enough flexibility for customization, extension, and mirroring. To solve these issues, we designed and developed a new KESM mouse brain atlas that uses a vector graphics format called Scalable Vector Graphics (SVG) instead of PNG, and OpenLayers API instead of Google Maps API. The SVG-based KESMBA using OpenLayers allows faster navigation and exploration of the KESM data, and more overlay of layers with the 4 times reduced file size compared to PNG tiles. Due to the reduced file size, the SVG-based KESMBA using OpenLayers is 2.45 times faster than the original atlas. By enhancing the performance, the users can more easily access the KESM data. We expect the SVG-based KESMBA to accelerate new discoveries in neuroscience.
  • The microstructure of the brain at the cellular level provides crucial information for the understanding of the function of the brain. A large volume of high-resolution brain image data from 3D microscopy is an essential resource to study detailed microstructures of the brain. Accordingly, we have worked on obtaining high-resolution image data of entire mouse brains using the Knife-Edge Scanning Microscope (KESM). Furthermore, to disseminate these high-resolution whole mouse brain data sets to the neuroscience research community, we developed a web-based brain atlas, the KESM Brain Atlas (KESMBA). To visualize the data sets in 3D while using only a standard web browser, we employed distance attenuation and Google Maps API. The KESMBA is a powerful tool to analyze and share the KESM mouse brain data sets, but the image loading was slow because of the number of raster image (PNG) tiles and the file size. Moreover, since Google Maps API is governed by a commercial license, it does not provide enough flexibility for customization, extension, and mirroring.

    To solve these issues, we designed and developed a new KESM mouse brain atlas that uses a vector graphics format called Scalable Vector Graphics (SVG) instead of PNG, and OpenLayers API instead of Google Maps API. The SVG-based KESMBA using OpenLayers allows faster navigation and exploration of the KESM data, and more overlay of layers with the 4 times reduced file size compared to PNG tiles. Due to the reduced file size, the SVG-based KESMBA using OpenLayers is 2.45 times faster than the original atlas. By enhancing the performance, the users can more easily access the KESM data. We expect the SVG-based KESMBA to accelerate new discoveries in neuroscience.

publication date

  • August 2013