Trace Editor/Features

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(Feature computation for Trace Editor)
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='''Feature List'''=
 
='''Feature List'''=
  
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{| border="1px" cellpadding="3" style="text-align:left"
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{| border="1px" cellpadding="2" style="text-align:left"
 
! Feature
 
! Feature
 
! Description
 
! Description
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='''Algorithms'''=
 
='''Algorithms'''=
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The algorithms suggested are used to control the editing process allowing for rule based cluster editing.
+
The algorithms suggested are used to control the editing process allowing for rule based cluster editing. The Goal is to complete group editing in five steps.  
−
=='''Merge'''==
+
[[Image:Edit_Operations.png|800px|thumb|center|Proposed steps of editing ]]
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 +
1: '''Merge Small Gaps'''
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Goal: Create longest continuous trace segments by merging close endpoints
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Methods: Nearest neighbors  (Closest end points), Rejection based on conflicts and thresholds
 +
 
 +
*Minimal distance between end points
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**Angle between traces
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**Path length
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**Gap distance is too large
 +
*Another trace is a better fit (Cost Function)
 +
**Smallest gap
 +
**Better Angular alignment
 +
*"Bad merge"
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**The merge causes corners
 +
**Needs to be smoothed
 +
 
 +
2: '''Interpolate Large Gaps'''
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Goal: Connect Large gaps that step 1 cannot  simply connect by addition of a  single cell
 +
Method: Larger gaps need new segments created, new Trace Bits must be added, smoothing operator.
 +
 
 +
*Curve fitting to find trend of:
 +
**Direction
 +
**Curvature
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*Interpolation
 +
**Extend the line
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**Most probable vector
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**Avoid  creating edges
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 +
[[Image:MergingBranching.gif|800px|thumb|right|Example showing how Merging and branching are interconnected. The Merging that creates sharp turns needs to be smoothed. The Traces need to create a new branch point and trace bits to interpolate the original path of the branch.]]
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3: '''Branch Points'''
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Goal: Detect and control Branching
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Method: Detect most probable intercepts, Determination of main branch and child, Type of branch point
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 +
*Distance maps
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**Nearest neighbors (traces)
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**Closest trace bits
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*Angle of intercept
 +
*Interpolation
 +
 
 +
4: '''Soma Detection'''
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Goal: Correspond processes with a soma
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Method: Segmentation of original data, Localize the area to attach processes to soma, Correct direction of traces
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 +
*Image intensity
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*Blob segmentation
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*Centroid
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*Distance map
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*Connectivity
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**Connected components
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**Localization of processes
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 +
[[Image:FullConnections.gif|800px|thumb|center|Illustration of how the processes should be connected to a soma(shown in red). <br />The Dendrites are shown in blue, where the axon is shown in yellow.]]
 +
 
 +
5: '''Fragments'''
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Goal: Removal of small traces that do not correspond to a process
 +
Method: Small traces removed, Leftovers from splitting operators, Line fragments that cannot be merged
 +
 
 +
*Lowest percentile of length
 +
**Traces with no parents or children
 +
**Type dependent

Revision as of 16:37, 24 June 2009

Feature computation for Trace Editor

Feature List

Feature Description
Gap Size Minimum distance between endpoints of two traces
Angle Is the angle created between two traces normalized as vectors
Path Length Total length along a trace, indicated by the size of the trace
Euclidean Distance Straight line distance between the endpoints of a trace
Fragmentation Smoothness Ratio of Path Length to Euclidean Distance[1]

Algorithms

The algorithms suggested are used to control the editing process allowing for rule based cluster editing. The Goal is to complete group editing in five steps.

Proposed steps of editing
1: Merge Small Gaps
Goal: Create longest continuous trace segments by merging close endpoints
Methods: Nearest neighbors  (Closest end points), Rejection based on conflicts and thresholds
  • Minimal distance between end points
    • Angle between traces
    • Path length
    • Gap distance is too large
  • Another trace is a better fit (Cost Function)
    • Smallest gap
    • Better Angular alignment
  • "Bad merge"
    • The merge causes corners
    • Needs to be smoothed 
2: Interpolate Large Gaps
Goal: Connect Large gaps that step 1 cannot  simply connect by addition of a  single cell
Method: Larger gaps need new segments created, new Trace Bits must be added, smoothing operator.
  • Curve fitting to find trend of:
    • Direction
    • Curvature
  • Interpolation
    • Extend the line
    • Most probable vector
    • Avoid creating edges
Example showing how Merging and branching are interconnected. The Merging that creates sharp turns needs to be smoothed. The Traces need to create a new branch point and trace bits to interpolate the original path of the branch.
3: Branch Points
Goal: Detect and control Branching
Method: Detect most probable intercepts, Determination of main branch and child, Type of branch point
  • Distance maps
    • Nearest neighbors (traces)
    • Closest trace bits
  • Angle of intercept
  • Interpolation 
4: Soma Detection
Goal: Correspond processes with a soma
Method: Segmentation of original data, Localize the area to attach processes to soma, Correct direction of traces
  • Image intensity
  • Blob segmentation
  • Centroid
  • Distance map
  • Connectivity
    • Connected components
    • Localization of processes
Illustration of how the processes should be connected to a soma(shown in red).
The Dendrites are shown in blue, where the axon is shown in yellow.
5: Fragments
Goal: Removal of small traces that do not correspond to a process
Method: Small traces removed, Leftovers from splitting operators, Line fragments that cannot be merged
  • Lowest percentile of length
    • Traces with no parents or children
    • Type dependent

Cite error: <ref> tags exist, but no <references/> tag was found
Retrieved from "http://farsight-toolkit.ee.uh.edu/wiki/Trace_Editor/Features"
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