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Team XYZ: Yan Xu Yu Zhang

Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

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Page 1: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Team XYZ: Yan Xu Yu Zhang

Page 2: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Imaging Processing

Communications

Group A at place AGroup B at place B

(thousands of miles away)

Long distance, Low efficiency

Page 3: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

CommandsResults

Group A Group B

YX

YZ

Hadoop

Page 4: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

• Pipeline I (projection, non-overlapping patches):

• 3D Image Storage: 2D Z slices in jpg

• Libraries: HIPI (FloatImage, JPEGFileInputFormat).

(xy index, FloatImage)

non-overlap XY patches

projection along z

merge to one projected jpg

Jpg seq

same xyindex

2D Z slices Projected Image

Page 5: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

• Pipeline II (3-D filtering, overlapping patches):

(xy index, FloatImage)

overlap XY patches

3-D image filtering

non-overlap XY patches

merge XY patches

(z index, FloatImage)

Jpg seqnamed by xy_z.jpg

Jpg seq

Jpg seq

same xyindex

same Z index

2D Z slicesof original 3D

image

2D Z slicesof processed

3D image

Page 6: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

190 jpg sequencesfor one 3-D image

(54.6MB, 1000 × 1000)Cropped into

5 × 5 patches (200 × 200) )

localhost:50030

Max Projection Mean Projection

Test 3-D image:

Page 7: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Web Terminal

Image Window

Control Panel

Display original 3D imageExplore 3D image by slicesZoom in and outHand moveDisplay processing result

Page 8: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Tools

Map-reduce

Java

Javascript

O

Page 9: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Compatibility

Compatible with ImageJ (open-source Java image processing tool)

Extendibility

Upload and run the script by users

Attractiveness

More user-friendly interface

Page 10: Cloud-based Storage, Processing and Rendering for Gegabytes 3D Biomedical Images

Team XYZ

XY YZ