Imaging Considerations to Enhance Data Post- Processing Trevor - - PowerPoint PPT Presentation

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Imaging Considerations to Enhance Data Post- Processing Trevor - - PowerPoint PPT Presentation

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Imaging Considerations to Enhance Data Post- Processing Trevor Lancon 2/29/2016 Commonly Asked Questions What are the hardware requirements for Amira/Avizo? How much RAM do I need? How can I work more efficiently with large data?

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Imaging Considerations to Enhance Data Post- Processing

Trevor Lancon

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Commonly Asked Questions

  • What are the hardware requirements for Amira/Avizo?
  • How much RAM do I need?
  • How can I work more efficiently with large data?

→ File size

2 Confidential

2/29/2016

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Example of How Avizo and Amira Utilize Hardware

How are hardware components utilized in this example?

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Hard Drive RAM VRAM CPU

Original Dataset Copy of Dataset 2D Visualization Filtering Algorithm Filtered Dataset 3D Visualization 1 2 3 4 5

Example of How Avizo and Amira Utilize Hardware

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SLIDE 5

5 Confidential

2/29/2016

  • 1. Open data
  • 2. Ortho Slice
  • 3. Median Filter
  • 4. Volren

1 3 4 2

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File Size

1. Load data 2. Slice alignment 3. Smoothing filter 4. Sharpening filter 5. Background correction 6. FFT filter

Confidential 6

Example DualBeam Workflow

2/29/2016

6x original in RAM!

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File Size

  • Small structures: high resolution
  • Statistics: large FOV

– Reject poor samples in post- analysis filtering – Reject 70% of 15 grains vs. – Reject 70% of 4000 grains

  • Coarseness of histogram bins
  • Image contrast
  • Larger affect on file size

Confidential 7

FOV / Resolution Bit Depth

2/29/2016

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File Size

8 Confidential

Consider 1500 x 1286 x 1040 Voxels

2/29/2016

1.9 3.7 7.5

1 2 3 4 5 6 7 8 100% 90% 80% 70% 60% 50% 40%

File Size [GB] FOV or Resolution [% of original size]

8bit 16bit float

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File Size

1. Load 16-bit data 2. Manage file size 3. Slice alignment 4. Smoothing filter 5. Sharpening filter 6. Background correction 7. FFT filter

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Example DualBeam Workflow

2/29/2016

15.1 16.9 22.2

5 10 15 20 25 Convert to 8bit Crop 60% None

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Commonly Asked Questions

  • What are the hardware requirements for Amira/Avizo?
  • How much RAM do I need?
  • How can I work more efficiently with large data?

→ File size

  • WHY IS SEGMENTATION SO HARD?!

→ Contrast

10 Confidential

2/29/2016

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Contrast

  • Segmentation depends on contrast

– Thresholding, watershed, morphology, etc.

  • Other factors affect contrast

– Probe (e.g. electrons) – Signal collection (e.g. camera exposure)

  • Optimize current vs. stage drift
  • Optimize dwell time / frame averaging vs. scan time

– Scan time vs. segmentation time

  • Reducing bit depth may reduce contrast?

11 Confidential

2/29/2016

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Contrast

Confidential 12

2/29/2016

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Contrast

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8 Bit – Normalized 16 Bit – Normalized

2/29/2016

17 34 51 68 85 102 119 136 153 170 187 204 221 238 255 4369 8738 13107 17476 21845 26214 30583 34952 39321 43690 48059 52428 56797 61166 65535

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Contrast

100 120 140 160 180 200 220 2000 2400 2800 3200 3600 4000 4400

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8 Bit 16 Bit

2/29/2016

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Contrast

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8 Bit – Thresholded (168) 16 Bit – Thresholded (3341)

2/29/2016

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Contrast

Confidential 16

8 Bit – Thresholded (168) 16 Bit – Thresholded (3341)

2/29/2016

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Contrast

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8 Bit – Watershed 16 Bit – Watershed

2/29/2016

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Thank you FIBSEM UGM!