Common Tracing Output Format
(New page: ==SWC Format== This format is described in detail in Ascioli ''et al.'''s work.<ref><span class="plainlinks">[http://www.jstor.org/stable/3067144 Giorgio A. Ascoli, Jeffrey L. Krichmar, Sl...) |
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| + | ==Introduction== | ||
| + | In this page we describe a common format for the tracing output that covers different image topologies (blood vessels, neuronal arbor with or without soma(s), spiny neuronal dendrites as well as branching). By common we mean all tracing tools inside [[Main_Page|FARSIGHT]]. In an effort to promote standardization, this format complies with SWC <ref name="ascioli" />. | ||
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==SWC Format== | ==SWC Format== | ||
| − | This format is described in detail in Ascioli ''et al.'''s work.<ref><span class="plainlinks">[http://www.jstor.org/stable/3067144 Giorgio A. Ascoli, Jeffrey L. Krichmar, Slawomir J. Nasuto, Stephen L. Senft. "Generation, Description and Storage of Dendritic Morphology Data", Philosophical Transactions: Biological Sciences, Vol. 356, No. 1412, Neuroscience Databases: Tools for Exploring Brain Structure-Function Relationships (Aug. 29, 2001), pp. 1131-1145] </span></ref> | + | This format is described in detail in Ascioli ''et al.'''s work.<ref name="ascioli"><span class="plainlinks">[http://www.jstor.org/stable/3067144 Giorgio A. Ascoli, Jeffrey L. Krichmar, Slawomir J. Nasuto, Stephen L. Senft. "Generation, Description and Storage of Dendritic Morphology Data", Philosophical Transactions: Biological Sciences, Vol. 356, No. 1412, Neuroscience Databases: Tools for Exploring Brain Structure-Function Relationships (Aug. 29, 2001), pp. 1131-1145] </span></ref> |
| + | The tree topology has to be preserved regardless of the tracing method or order of its results. Therefore, any soma or branch points are assumed to be segmented and available as part of the algorithm output. | ||
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| + | ;Every SWC line (representing a dendrite, blood vessel, or a part thereof) is a potential parent and has: | ||
| + | # a unique ID (1st column or field) | ||
| + | # a type descriptor (2nd column T: 1=Soma, 3=dendrite) | ||
| + | # the <math>x,y,z</math> coordinates of the starting point | ||
| + | # a Connectivity index (to which this segment is connected in a direction leading to the tree top | ||
| + | #* The tree top is either the soma (if available) or the starting line. | ||
| + | #* The tree top has ID=1 and connectivity index= -1 | ||
| + | #* A tracing segment may connect back to the top (ID=1) or to another segment via its ID. | ||
==Tracing Output in Compliance with SWC == | ==Tracing Output in Compliance with SWC == | ||
| + | The tracing algorithms in [[Main_Page|FARSIGHT]] may contain more details than the minimal SWC requirements. Such details are center points in every trace line, spines protruding from dendrites and possibly other features or information. Therefore, we consider the line as a parent and its trace points as children. | ||
| + | ;Assumptions: we know the following | ||
| + | *existence of soma and its branches | ||
| + | *dendritic branch points accurate to the tracing segment resolution | ||
| + | *spines (if applicable) | ||
| + | ;After a line is declared, the center-points (referred to as TraceBits) are listed: | ||
| + | # | ||
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| + | (Example from Fig1 below: ID=2 is a dendrite segment connecting to soma; ID=8 is a dendrite segment connecting to ID=4- a dendrite segment.) | ||
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| + | • Parent types are Soma (S), Dendrite (D), (may add more if needed). | ||
| + | • Tags are soma, traceline, tracebit, spine | ||
| + | • ID and object tag identify the XML line (object) uniquely. | ||
| + | • The IDs are unique only within their tree/type level. | ||
| + | • If there is one or more soma, each has its line, type, and ID: | ||
| + | <Soma ID=1 ParentID=-1 X=-1.5 Y=-8.2 Z=1.3 Width1=3.8> | ||
| + | • A dendrite (tag= TraceLine) is a collection of segments (tag=TraceBit) | ||
| + | • A dendrite may branch off of a soma or another dendrite. | ||
| + | o This is identified by its ParentType=S or D, and ParentID=number. | ||
| + | o If the ParentType=D, then it must have branched from a segment at BranchTraceBit=number. | ||
| + | • Each dendrite segment (tag=TraceBit) has its unique ID within the TraceLine. | ||
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==Example == | ==Example == | ||
Revision as of 16:27, 15 May 2009
Contents |
Introduction
In this page we describe a common format for the tracing output that covers different image topologies (blood vessels, neuronal arbor with or without soma(s), spiny neuronal dendrites as well as branching). By common we mean all tracing tools inside FARSIGHT. In an effort to promote standardization, this format complies with SWC [1].
SWC Format
This format is described in detail in Ascioli et al.'s work.[1] The tree topology has to be preserved regardless of the tracing method or order of its results. Therefore, any soma or branch points are assumed to be segmented and available as part of the algorithm output.
- Every SWC line (representing a dendrite, blood vessel, or a part thereof) is a potential parent and has
- a unique ID (1st column or field)
- a type descriptor (2nd column T: 1=Soma, 3=dendrite)
- the x,y,z coordinates of the starting point
- a Connectivity index (to which this segment is connected in a direction leading to the tree top
- The tree top is either the soma (if available) or the starting line.
- The tree top has ID=1 and connectivity index= -1
- A tracing segment may connect back to the top (ID=1) or to another segment via its ID.
Tracing Output in Compliance with SWC
The tracing algorithms in FARSIGHT may contain more details than the minimal SWC requirements. Such details are center points in every trace line, spines protruding from dendrites and possibly other features or information. Therefore, we consider the line as a parent and its trace points as children.
- Assumptions
- we know the following
- existence of soma and its branches
- dendritic branch points accurate to the tracing segment resolution
- spines (if applicable)
- After a line is declared, the center-points (referred to as TraceBits) are listed
(Example from Fig1 below: ID=2 is a dendrite segment connecting to soma; ID=8 is a dendrite segment connecting to ID=4- a dendrite segment.)
• Parent types are Soma (S), Dendrite (D), (may add more if needed). • Tags are soma, traceline, tracebit, spine • ID and object tag identify the XML line (object) uniquely. • The IDs are unique only within their tree/type level. • If there is one or more soma, each has its line, type, and ID: <Soma ID=1 ParentID=-1 X=-1.5 Y=-8.2 Z=1.3 Width1=3.8> • A dendrite (tag= TraceLine) is a collection of segments (tag=TraceBit) • A dendrite may branch off of a soma or another dendrite. o This is identified by its ParentType=S or D, and ParentID=number. o If the ParentType=D, then it must have branched from a segment at BranchTraceBit=number. • Each dendrite segment (tag=TraceBit) has its unique ID within the TraceLine.
Example
Sample XML
References
- ↑ 1.0 1.1 Giorgio A. Ascoli, Jeffrey L. Krichmar, Slawomir J. Nasuto, Stephen L. Senft. "Generation, Description and Storage of Dendritic Morphology Data", Philosophical Transactions: Biological Sciences, Vol. 356, No. 1412, Neuroscience Databases: Tools for Exploring Brain Structure-Function Relationships (Aug. 29, 2001), pp. 1131-1145
