open_fafb_ngl: Construct Neuroglancer URL based on 3D location data

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

Construct Neuroglancer URL based on 3D location data

Description

Construct Neuroglancer URL based on 3D location data

Usage

open_fafb_ngl(
  x,
  s = rgl::select3d(),
  zoomFactor = 8,
  coords.only = FALSE,
  open = interactive() && !coords.only,
  sample = NULL,
  reference = NULL,
  sampleurl = NULL,
  ...
)

Arguments

x	A numeric vector OR any object compatible with xyzmatrix OR a CATMAID URL (see details)
s	Optional selection function of the type returned by select3d
zoomFactor	The Neuroglancer zoomFactor (bigger means zoomed out)
coords.only	Return raw coordinate string for pasting into Neuroglancer position widget (top left of screen)
open	Whether or not to open the URL in a browser - this defaults to TRUE in interactive use.
sample, reference	Template space of the input object sample and target (reference). See examples and xform_brain for details of how these are specified.
sampleurl	A sample URL that defines your Neuroglancer dataset.
...	Additional arguments passed to fromJSON to control JSON parsing.

Details

Neuroglancer scenes seem to be specified in a single URL that encodes a json object defining layers to display, position etc. This function works by taking a sample URL defining such a scene and then editing it to point to a new 3D location / adjust zoom.

This package comes with 4 different default scene urls specified via choose_segmentation or with_segmentation. This is the easiest way to choose a particular segmentation. You can also specify a different sample URL via the sampleurl argument; it will be remembered for the rest of the R session. If you regularly use a particular kind of scene URL, you can set options(fafbseg.sampleurl) in your Rprofile file.

Value

A character vector with a Neuroglancer URL or coordinate string (invisibly when open=TRUE)

See Also

Other neuroglancer-urls: flywire_ids(), flywire_scene(), ngl_blank_scene(), ngl_decode_scene(), ngl_encode_url(), ngl_segments()

Examples

u=paste0("https://fafb.catmaid.virtualflybrain.org/?pid=2&zp=131280&",
"yp=170014.98879622458&xp=426584.81386896875&tool=navigator&sid0=2&s0=-1")

# translate URL but don't open browser
open_fafb_ngl(u, open=FALSE)

# produce an x,y,z string to paste into Neuroglancer
open_fafb_ngl(u, coords.only=TRUE)

# translate URL converting from FAFB14 to FlyWire coordinates
# (only a small shift)
open_fafb_ngl(u, sample="FAFB14", reference="FlyWire", open=FALSE)
## Not run: 
# copy CATMAID URL from clipboard and Neuroglancer coords to clipboard
clipr::write_clip(open_fafb_ngl(clipr::read_clip(), coords.only=TRUE))

# Open a location in MB peduncle with current preferred segmentation
open_fafb_ngl(c(433440, 168344, 131200))

# choose a particular segmentation (Google FAFB)
with_segmentation("20190805", open_fafb_ngl(c(433440, 168344, 131200),
zoomFactor=2))

# or FlyWire
with_segmentation("flywire", open_fafb_ngl(c(433440, 168344, 131200)))

# ... and translate FAFB14 to FlyWire coordinates
with_segmentation("flywire", open_fafb_ngl(c(433440, 168344, 131200),
sample="FAFB14", reference="FlyWire", zoomFactor=2))

# open a CATMAID URL in Neuroglancer
open_fafb_ngl(u)

# Set an existing scene URL (pointing to any old location) to act as
# the template for open_fafb_ngl
# nb the package sets one for you on startup if you haven't set yourself
options(fafbseg.sampleurl="https://<neuroglancerlurl>")
# Edit your R profile if you want to set a different default
usethis::edit_r_profile()

## End(Not run)

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