Trace Editor/Features
From FarsightWiki
(Difference between revisions)
m (→Algorithms) |
|||
| Line 29: | Line 29: | ||
1: '''Merge Small Gaps''' | 1: '''Merge Small Gaps''' | ||
Goal: Create longest continuous trace segments by merging close endpoints | Goal: Create longest continuous trace segments by merging close endpoints | ||
| − | Methods: Nearest neighbors (Closest end points), Rejection based on conflicts and thresholds | + | Methods: Nearest neighbors (Closest end points), <br />Rejection based on conflicts and thresholds |
*Minimal distance between end points | *Minimal distance between end points | ||
| Line 44: | Line 44: | ||
2: '''Interpolate Large Gaps''' | 2: '''Interpolate Large Gaps''' | ||
Goal: Connect Large gaps that step 1 cannot simply connect by addition of a single cell | 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. | + | Method: Larger gaps need new segments created, <br />new Trace Bits must be added, <br />smoothing operator. |
| + | [[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 | ||
*Curve fitting to find trend of: | *Curve fitting to find trend of: | ||
**Direction | **Direction | ||
| Line 53: | Line 54: | ||
**Most probable vector | **Most probable vector | ||
**Avoid creating edges | **Avoid creating edges | ||
| − | + | path of the branch.]] | |
| − | + | ||
3: '''Branch Points''' | 3: '''Branch Points''' | ||
Goal: Detect and control Branching | Goal: Detect and control Branching | ||
| − | Method: Detect most probable intercepts, Determination of main branch and child, Type of branch point | + | Method: Detect most probable intercepts, <br />Determination of main branch and child, <br />Type of branch point |
*Distance maps | *Distance maps | ||
| Line 67: | Line 67: | ||
4: '''Soma Detection''' | 4: '''Soma Detection''' | ||
Goal: Correspond processes with a soma | Goal: Correspond processes with a soma | ||
| − | Method: Segmentation of original data, Localize the area to attach processes to soma, Correct direction of traces | + | Method: Segmentation of original data, <br />Localize the area to attach processes to soma, <br />Correct direction of traces |
*Image intensity | *Image intensity | ||
| Line 81: | Line 81: | ||
5: '''Fragments''' | 5: '''Fragments''' | ||
Goal: Removal of small traces that do not correspond to a process | 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 | + | Method: Small traces removed, <br />Leftovers from splitting operators, <br />Line fragments that cannot be merged |
*Lowest percentile of length | *Lowest percentile of length | ||
**Traces with no parents or children | **Traces with no parents or children | ||
**Type dependent | **Type dependent | ||
Revision as of 21:17, 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.
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.
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
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
