Pick the principal branch point of a neuron (useful for annotation tables)

`key_point_from_neuron()` picks a good "key" point on an in-memory neuron — the principal branch point of its skeleton — suitable for hanging an annotation off (e.g. a point column in an annotation table).

`flywire_key_point()` is a convenience wrapper that reads the L2 skeleton for one or more flywire-style root ids and returns the key point of each.

Usage

key_point_from_neuron(n, reroot = TRUE)

flywire_key_point(ids, raw = TRUE, reroot = TRUE, ...)

Arguments

n

A `neuron` (typically an L2 skeleton).

reroot

Whether to reroot onto the furthest endpoint before simplifying.

ids

One or more flywire-style root ids (anything accepted by [read_l2skel()]).

raw

Whether to return points in raw (voxel) space (default) or nm.

...

Additional arguments passed to [pbapply::pbsapply()].

Value

`key_point_from_neuron()` returns a length-3 nm xyz vector. `flywire_key_point()` returns an N x 3 matrix of points (one row per input id), in raw voxel space unless `raw=FALSE`.

Details

The point sits at the major branch point of the (L2) skeleton. By default the neuron is first rerooted onto the endpoint furthest from the current root, so that simplifying to a single branch point is well-defined (otherwise the longest path from the root may contain no branch point at all). If no branch point can be found the original root point is returned as a fallback.

`flywire_key_point()` reads each skeleton with [read_l2skel()], whose dataset is selected by the ambient cave/segmentation context; wrap the call in a helper such as `with_crant()` (crantr) or `with_aedes()` (aedes) to target a non-default segmentation.

See also

[read_l2skel()]

Examples

if (FALSE) { # \dontrun{
n <- read_l2skel('720575940621039145')[[1]]
key_point_from_neuron(n)

flywire_key_point('720575940621039145')
} # }