Choose or (temporarily) use a FAFB autosegmentation — choose

with_segmentation allows a specific segmentation to be temporarily selected.

Usage

choose_segmentation(
  release = c("flywire31", "public-flywire31", "20200412", "20190805", "20190521",
    "sandbox-flywire31"),
  set = TRUE,
  moreoptions = list()
)

with_segmentation(release, expr)

Arguments

release: character vector specifying a released segmentation via a known short name or a sample neuroglancer URL.
set: Whether or not to set the selected options for the selected release.
moreoptions: Any further options that you might wish to set (optional, expert use only, principally intended for use by fancr package).
expr: The expression to execute with the temporary options set

Value

If set=TRUE a list containing the previous values of the relevant global options (in the style of options. If set=FALSE a named list containing the option values.

The result of evaluating expr

Details

Each released segmentation implies a number of global options. This package comes with multiple different default scene urls specified via choose_segmentation or with_segmentation. This is the easiest way to choose a particular segmentation. You can also pass a sample URL to the release argument.

As of Nov 2020, the "flywire31" is the default segmentation when the package loads. This specifies the production (i.e. in progress) version of the flywire dataset. You will need to register with the flywire team and generate a flywire token linked to the email used during your registration to access this. Alternatively you can also use the "public-flywire31" data release accompanying the Dorkenwald et al 2023 and Schlegel et al 2023 publications; you still need a token for this (see flywire_set_token), but no registration is required (and there are no limitations on use of these data for new projects besides citing those two preprints).

You can also specify a different sample URL via the sampleurl argument of some functions; 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.

If you need to use both built-in and custom segmentation URLs, we recommend specifying the custom URL in your Rprofile file and using the with_segmentation to run code that uses one of the built-in segmentations.

Examples

# \donttest{
choose_segmentation('20190805', set=FALSE)
#> $fafbseg.sampleurl
#> [1] "https://neuroglancer-demo.appspot.com/#!%7B%22layers%22:%5B%7B%22source%22:%22precomputed://gs://neuroglancer-fafb-data/fafb_v14/fafb_v14_clahe_sharded%22%2C%22type%22:%22image%22%2C%22name%22:%22fafb_v14_clahe%22%7D%2C%7B%22source%22:%22brainmaps://772153499790:fafb_v14:fafb-ffn1-20190805%22%2C%22type%22:%22segmentation%22%2C%22skeletonRendering%22:%7B%22mode2d%22:%22lines_and_points%22%2C%22mode3d%22:%22lines%22%7D%2C%22name%22:%22fafb-ffn1-20190805%22%7D%2C%7B%22source%22:%22brainmaps://772153499790:fafb_v14:fafb-ffn1-20190805-skeletons32nm%22%2C%22type%22:%22segmentation%22%2C%22segments%22:%5B%220%22%5D%2C%22skeletonRendering%22:%7B%22mode2d%22:%22lines_and_points%22%2C%22mode3d%22:%22lines%22%7D%2C%22name%22:%22fafb-ffn1-20190805-skeletons32nm%22%7D%5D%2C%22navigation%22:%7B%22pose%22:%7B%22position%22:%7B%22voxelSize%22:%5B4%2C4%2C40%5D%2C%22voxelCoordinates%22:%5B122437.5625%2C36391.234375%2C2057.085205078125%5D%7D%7D%2C%22zoomFactor%22:8%7D%2C%22perspectiveOrientation%22:%5B-0.6771116256713867%2C0.6536111831665039%2C-0.1610027700662613%2C0.2973051071166992%5D%2C%22perspectiveZoom%22:5184.860830857428%2C%22showSlices%22:false%2C%22layout%22:%224panel%22%7D"
#> 
#> $fafbseg.skeletonuri
#> [1] "brainmaps://772153499790:fafb_v14:fafb-ffn1-20190805-skeletons32nm"
#> 
#> $fafbseg.brainmaps.volume
#> [1] "772153499790:fafb_v14:fafb-ffn1-20190805"
#> 
#> $fafbseg.brainmaps.meshName
#> [1] "mcws_quad1e6"
#> 
#> $fafbseg.catmaid
#> [1] "https://garden.catmaid.org/tracing/fafb/v14-seg-li-190805.0/"
#> 
#> $fafbseg.cloudvolume.url
#> [1] "brainmaps://772153499790:fafb_v14:fafb-ffn1-20190805"
#> 
# }
if (FALSE) { # \dontrun{
# temporarily change default segmentation to run a command
# but restore original default when finished
# Choose the FlyWire segmentation
with_segmentation('flywire31', {open_fafb_ngl(c(460792, 221812, 61480))})

# similarly for one Google (Li and Jain) segmentation
with_segmentation('20190805', {open_fafb_ngl(c(460792, 221812, 61480))})
} # }
if (FALSE) { # \dontrun{
n <- with_segmentation("20190521",
  read.neuron.brainmaps(22427007374))

# open location in flywire
with_segmentation("flywire", open_fafb_ngl(c(433440, 168344, 131200)))
} # }