Extract annotations from a neuroglancer scene into a dataframe

Extract annotations from a neuroglancer scene into a dataframe

Usage

ngl_annotations(
  x,
  layer = NULL,
  types = c("point", "line"),
  points = c("collapse", "expand", "list")
)

Arguments

x

A neuroglancer scene or URL (passed to ngl_decode_scene as necessary) or a neuroglancer layers (nglayers) extracted from such a scene.

layer

Optional index vector specifying the layers within a scene from which to extract annotations. It is probably safest to use a character vector of layer names (what appears in neuroglancer). When missing all annotation layers are processed.

types

Which annotation types to process (currently only points and lines by default)

points

What to do with point coordinates.

Value

A data.frame with columns defined by the contents of the annotation layer and the types/points arguments. Additional annotation features are stored as attributes on the data.frame.

See also

ngl_annotation_layers to make new annotation layers

Examples

# \donttest{
u="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5963849085747200"
adf=ngl_annotations(u)
str(attr(adf, 'ann_attrs'))
#> List of 1
#>  $ lines:List of 9
#>   ..$ tool                                : chr "annotatePoint"
#>   ..$ selectedAnnotation                  :List of 1
#>   .. ..$ id: chr "c8e65c47e6677d4dcb2bc2846c26ec4b277756c4"
#>   ..$ type                                : chr "annotation"
#>   ..$ annotationTags                      :List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ id   : int 1
#>   .. .. ..$ label: chr "good"
#>   .. ..$ :List of 2
#>   .. .. ..$ id   : int 2
#>   .. .. ..$ label: chr "bad"
#>   .. ..$ :List of 2
#>   .. .. ..$ id   : int 3
#>   .. .. ..$ label: chr "ok"
#>   ..$ voxelSize                           : int [1:3] 4 4 40
#>   ..$ linkedSegmentationLayer             : chr "Production-segmentation_with_graph"
#>   ..$ bracketShortcutsShowSegmentation    : logi FALSE
#>   ..$ annotationSelectionShowsSegmentation: logi FALSE
#>   ..$ name                                : chr "lines"
# }