Sam AnzarootResearcher

Dr. Yoonsuck ChoeDr. John KeyserFaculty Mentors

Huei-Fang YangGraduate Student Mentor

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Knife-Edge Scanning Microscope at Brain Networks Lab

The Knife Edge Scanning MicroscopeRendering of Imaging Process and Image of Epoxy Encased Mouse Brain.

How can this data be released to the public?

Users need to be able to easily browse the data in three Users need to be able to easily browse the data in three

dimensions.dimensions. The interface should be accessible to a large user base.The interface should be accessible to a large user base. The application needs to allow for the labeling of 3D The application needs to allow for the labeling of 3D

regions with expert information.regions with expert information.

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Resulting Volumetric Image Stack

Web Based Map Project

Screenshot of the zoomable web based browser implemented using HTML, CSS, and JavaScript.

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Step 1:Each layer is resized into many zoom levels.

Step 2:Each resized image is cropped into 256x256 Pixel segment images, and each image is named by its zoom and Pixel location.

Web Based Interface for Viewing and Annotating Volumetric Data

Time in Seconds

On Machine w/ Xeon 2.4 GHZ CPU and 4GB RAM using imagemagick.

Resizing and Cropping Speeds for One Layer with Different Image File Formats

Process Details

Resizing and cropping a dataset can take up to eleven days.Resizing and cropping a dataset can take up to eleven days.

The resizing process uses a combination of the scale and The resizing process uses a combination of the scale and

sample resizing algorithms with JPGs for best speed/quality.sample resizing algorithms with JPGs for best speed/quality.

The web interface calculates the current viewport range and The web interface calculates the current viewport range and

loads images based on filename information.loads images based on filename information.

Moving in the z direction is done by overlaying a selected Moving in the z direction is done by overlaying a selected

layer on top of current layer.layer on top of current layer.

Layers are segmented into columns which adds additional Layers are segmented into columns which adds additional

complications to the process.complications to the process.

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Annotation Details

Annotations facilitate the browsing of the data and allow for Annotations facilitate the browsing of the data and allow for

the collection of research information. the collection of research information.

Three types of implemented annotations are: Polygons, Three types of implemented annotations are: Polygons,

Polylines, and Point annotations.Polylines, and Point annotations.

Users need to be able to annotate 3D structures that can span Users need to be able to annotate 3D structures that can span

across hundreds of layers.across hundreds of layers.

Each annotation has associated name and tagging Each annotation has associated name and tagging

information.information.

Annotations need to be stored in a shared database.Annotations need to be stored in a shared database.

Annotating requires cross-browser drawing technology.Annotating requires cross-browser drawing technology.

Volumetric Polygonal Annotation of a Blood Vessel Cross Section

Example 3D Structure in Image Stack

Annotation Process

The user can specify the top and bottom polygons and any The user can specify the top and bottom polygons and any number of necessary in-between polygons of a structurenumber of necessary in-between polygons of a structureand the software will perform a linear interpolation ofand the software will perform a linear interpolation ofthe polygonal points in order to estimate where the structurethe polygonal points in order to estimate where the structureis in a particular level.is in a particular level.

The user can then choose to store the annotation and itsThe user can then choose to store the annotation and itslabel into a shared database hosted at Texas A&M or label into a shared database hosted at Texas A&M or download the data so that it can be seen by other people download the data so that it can be seen by other people using the interface.using the interface.

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This research has resulted in:

• The creation of an open JavaScript application that can

efficiently display volumetric image stack data.

• The invention of a system that allows for the annotation of

three-dimensional structures using the image stack data

viewer.

The microscope scans complete organs of small animals (ex. Rat brains), and each scan produces thousands of high-resolution images. The size of a compressed dataset can reach up to hundreds of gigabytes.

Acknowledgements:

Many thanks to: Dr. Yoonsuck Choe and Dr. John Keyser for their mentorship and guidance, the graduate students in the lab, including Huei-Fang Yang, Timothy Mann, David Mayerich, Donghyeop Han, and Jae Rock Kwon. This research was done with the help of NINDS, NSF, Texas ARP funding, and NSF REU funding

References:

Brain Networks Laboratory:KESM. http://research.cs.tamu.edu/bnl/static/kesm.htmlImageMagick: Resizing, http://www.imagemagick.org/Usage/resize/

Possible further work on this project includes:

• The performance of a user study in order to determine the effectiveness of the user interface.

• The addition of optional three dimensional views using either future enhancements to the HTML specification or a third party plug-in.

• A computational analysis of the user inputted annotation data possibly for use in the validation of tracing algorithms.

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Interpolated Annotation

Annotated Layer

Annotated Layer