fafb_world_mapper: Convert coordinates between different FAFB assemblies

In natverse/elmr: Support for working with light and electron microscopy fly brain data

Convert coordinates between different FAFB assemblies

Description

fafb_world_mapper provides a low-level interface to map coordinates based on the tem-services API available from inside the HHMI Janelia VPN. The hope is to make this service generally available in due course.

End users are not presently expected to use this directly. Instead they should use xform_brain to transform data. See examples.

Usage

fafb_world_mapper(
  xyz,
  from,
  to,
  baseurl = paste0("http://tem-services.int.janelia.org:8080/render-ws/v1/",
    "owner/flyTEM/project/FAFB00/stack"),
  method = c("single", "many"),
  ...
)

Arguments

xyz	xyz coordinates (in nm)
from, to	Assemblies to convert between e.g. "v12", "v13", "v14".
baseurl	path to Janelia tem-services server (not externally visible at the moment)
method	Whether to try and convert multiple coordinates at once. Defaults to 'single'. The 'many' method currently appears fragile and not much faster.
...	Additional arguments (currently unused)

Examples

## Not run: 
FAFB12.surf=xform_brain(JFRC2013.surf, sample = JFRC2013, reference = FAFB12)
FAFB13.surf=xform_brain(JFRC2013.surf, sample=JFRC2013, ref=FAFB13)
# current assembly
FAFB.surf=xform_brain(JFRC2013.surf, sample=JFRC2013, ref=FAFB)

## End(Not run)

natverse/elmr documentation built on Sept. 2, 2023, 9:30 a.m.