flywire_voxdims: Handle raw and nm calibrated flywire coordinates

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Handle raw and nm calibrated flywire coordinates

Description

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.

Details

relies on nat >= 1.10.4

Value

For flywire_voxdims A 3-vector

for flywire_raw2nm and flywire_nm2raw an Nx3 matrix of coordinates

Examples

flywire_voxdims()
# ensure that we use default production flywire scene
with_segmentation('flywire', flywire_voxdims())
flywire_raw2nm(c(159144, 22192, 3560))
flywire_raw2nm('159144 22192 3560')
## Not run: 
flywire_nm2raw(clipr::read_clip())

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.