3D Segmentation of Neurons from Electron Micrographs

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3D Segmentation of Neurons from Electron
Micrographs

• Nathaniel Thomas
• under the direction of Prof. Sebastian Seung and
• Mr. Srinivas Turaga
• Research Science Institute 2006

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Neurons in the Brain

• Neuron function is the most fundamental level of
  brain function.
• Neurons interpret electrochemical signals from
  multiple other neurons and output a single on/off
  signal.
• The brain is essentially a large neural network.
• Fully understanding the brain requires schematics
  of the brains neural circuitry.

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Neural Circuitry Schematics

• We have 3D electron micrographs (EMs) of neurons
  in the brain.
• We want a schematic of the neural circuitry in
  the images.
• This requires finding the edges of neurons in the
  electron micrographs.

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Electron Micrographs of Neurons
Electron micrograph of rat retina tissue
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Edge Detection

• Canny Edge Detection Algorithm Outline
• Remove white noise.
• Apply an edge-detecting operator.
• Thin the detected edges to increase precision.
• Connect small discontinuities in edges using
  hysteresis.

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Step 1 Remove Noise

• 1D Gaussian filter

Before filter
Intensity
Space
After filter
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Step 2 Apply Operator
1D Image
Operator
Output
First Derivative of a Gaussian
Second Derivative of a Gaussian
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Step 3 Non-Maximum Suppression
With NMS
Without NMS
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Step 4 Hysteresis
Strong Edges
Weak Edges
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Neurons Identified in EMs
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3D Segmentation of Neurons
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Future Work

• Increase the precision of 3D segmentation by
  making more intelligent algorithms
• Algorithms might have prior knowledge about types
  of junctions between cells.
• Algorithms could identify sites of
  electrochemical interaction in the 3D
  segmentation to create neural schematics.

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Acknowledgements

• Many thanks to
• Professor Seung for the opportunity to work in
  his lab
• Mr. Srini Turaga for his guidance throughout this
  project
• The Center for Excellence in Education and the
  Massachusetts Institute of Technology for their
  efforts and resources supporting the Research
  Science Institute.