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Currently, TreeParser.setSkipSomaticSegments(true) only takes effect when the
soma is represented as a single-point path (i.e., soma.onPath.size() == 1). If
the soma path has more than one node, the flag is silently ignored (a warning is
now emitted as of the latest commit, but the segments are still included).
IIRC, the feature exists specifically for microglia and similar cells where the somatic
connector segments would otherwise inflate the innermost Sholl counts.
The question is whether the feature should be generalized to soma paths of any
length. Two possible interpretations:
- Skip the entire soma path regardless of node count, and skip the first
segment of primary paths that connect to it. This would be consistent with
the current intent - Skip only the segments that lie within the bounding extent of the soma
path (e.g., within its maximum radius), which would be geometrically more
principled but more involved to implement
Option 1 seems like the natural extension and a low-risk change!? Leaving it here
for discussion, and documentation of the current status
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