Soma positions and logical sides for fish2 neurons

fish_somapos returns the soma position of each requested body, preferring the somaLocation field and falling back to tosomaLocation where the former is missing.

fish_soma_side returns the logical side of each requested body in the dataset. The side may be derived from a manual annotation (when one exists), the instance name suffix, or the soma's position relative to the fish2 midline.

Usage

fish_somapos(
  ids,
  units = c("nm", "raw", "emraw", "microns"),
  as_character = FALSE
)

fish_soma_side(
  ids,
  method = c("auto", "manual", "instance", "position"),
  threshold = 0
)

Arguments

ids

Body ids, a query string (see fish_ids), or a metadata data.frame as returned by fish_neuprint_meta.

units

Units for the returned coordinates. The neuprint somaLocation / tosomaLocation values are stored in raw voxel coordinates; fish_coords converts to the requested units. "nm" (the default) scales by the fish2 raw voxel size (16, 16, 15); "raw" passes through; "emraw" returns the (8, 8, 30) nm acquisition grid; "microns" returns nm / 1000.

as_character

If TRUE, return a character vector of "x,y,z" strings (the fishr convention for location columns). Default FALSE.

method

One of "auto" (default), "manual", "instance", "position". See Details.

threshold

Absolute Y displacement (nm) below which position reports a soma as midline ("M"). Default 0. Ignored by instance and manual.

Value

fish_somapos returns an Nx3 numeric matrix with columns x, y, z, or a character vector of "x,y,z" strings when as_character = TRUE. Bodies that have neither somaLocation nor tosomaLocation produce NA rows.

fish_soma_side returns a character vector of "L", "R", "M", "U" or NA, one entry per input body.

Details

The "side" returned by fish_soma_side is the **logical** side of the neuron in the dataset, not necessarily the side of the physical soma. For an ascending fibre entering the brain through a nerve from outside the EM volume, the side reflects the entry point. Such a neuron may have its soma on one side of the cord and cross to the other side before entering the imaged volume; the assigned side will follow the entry nerve, not the soma.

Methods for fish_soma_side:

auto

Try manual first, then fill remaining NAs with instance, then with position.

manual

Read the neuprint somaSide column directly. Returns NA for bodies that do not have a manual assignment.

instance

Match _([LRMU])$ against the name (or instance) column.

position

Classify each soma by its signed displacement from the fish2 midline via fish_point_side. threshold is forwarded as-is; the default 0 means position never returns "M". "M" is reserved for bilaterally symmetric unpaired neurons that should be flagged by their instance suffix.

See also

fish_neuprint_meta, fish_point_side, mirror_fish

Other data-queries: fish_connection_table(), fish_ids(), fish_neuprint_meta(), register_fish_coconat()

Examples

# \donttest{
meta <- fish_neuprint_meta(109192746)
#> Warning: Clio dataset lookup failed; falling back to baked-in neuprint settings for `fish2`. Clio-backed functionality may be unavailable in this session.
fish_somapos(meta)
#>           X      Y      Z
#> [1,] 898128 426816 158175
fish_somapos(meta, units = "microns")
#>            X       Y       Z
#> [1,] 898.128 426.816 158.175
fish_soma_side(meta)
#> [1] "R"
# }