Handle raw and nm calibrated flywire coordinates

flywire_voxdims returns the image voxel dimensions which are normally used to scale between raw and nm coordinates.

Usage

flywire_voxdims(url = getOption("fafbseg.sampleurl"))

flywire_nm2raw(x, vd = flywire_voxdims())

flywire_raw2nm(x, vd = flywire_voxdims())

Arguments

url

Optional neuroglancer URL containing voxel size. Defaults to getOption("fafbseg.sampleurl") as set by choose_segmentation.

x

3D coordinates in any form compatible with xyzmatrix

vd

The voxel dimensions in nm. Expert use only. Normally found automatically.

Value

For flywire_voxdims A 3-vector

for flywire_raw2nm and flywire_nm2raw an Nx3 matrix of coordinates

Details

relies on nat >= 1.10.4

Examples

flywire_voxdims()
#> [1]  4  4 40
#> attr(,"units")
#> [1] "nm"
# ensure that we use default production flywire scene
with_segmentation('flywire', flywire_voxdims())
#> [1]  4  4 40
#> attr(,"units")
#> [1] "nm"
flywire_raw2nm(c(159144, 22192, 3560))
#>           X     Y      Z
#> [1,] 636576 88768 142400
flywire_raw2nm('159144 22192 3560')
#>           X     Y      Z
#> [1,] 636576 88768 142400
if (FALSE) { # \dontrun{
flywire_nm2raw(clipr::read_clip())
} # }