NeuroData Cloud

Programmatically annotate in R

When using neuroglancer to view your dataset you may want to add some point annotations to share with collaborators. The following will help you use R to do that.

Exporting neuroglancer state

When you have your neuroglancer window set the way you want it with all the channels and colors set accordingly use the export JSON functionality by clicking the {} in the upper right of the window and the click export. This will download a file called state.json. Place this file in the directory with your R script.

File setup

We'll read the JSON file into R as a list using the rjson package.

f <- file('state.json', 'r')
h <- rjson::fromJSON(file = f)
close(f)

Add an annotation layer

We'll need to grab some settings from the existing state and setup a new annotation layer, called MyAnnotations.

## grab voxel size of current navigation settings
voxelSize <- h$navigation$pose$positio$voxelSize

## grab current voxel coordinates
voxelCoordinates <- h$navigation$pose$positio$voxelCoordinates

## Create a new list for the new layer
MyAnnotations <- list(type = "annotation",
                      tool = "annotateSphere",
                      annotationColor = "#ff9900", # orange
                      voxelSize = as.numeric(voxelSize)
                     )

## Example of the structure for 2 ellipsoid annotations ##
##annotations <- list(list(center = c(6963, 7296.5, 23.5), 
##                         radii = c(68.2422180175781, 68.2422180175781, 4.09453296661377), 
##                         type = "ellipsoid", 
##                         id = "1", 
##                         description = "1"),
##                    list(center = c(6968, 7298, 23.5), 
##                         radii = c(80, 80, 8), 
##                         type = "ellipsoid", 
##                         id = "2", 
##                         description = "2"))

Function to format annotations

The following function takes x, y, z, and id parameters and uses the voxelSize to specify spherical annotations, you can change this if you want ellipsoidal annotations.

makeEllipse <- function(x, y, z, id, 
                        rx = 100/voxelSize[1], 
                        ry = 100/voxelSize[2], 
                        rz = 100/voxelSize[3], 
                        type = "ellipsoid", 
                        desc = id) {

  list(center = c(x, y, z), 
       radii = c(rx, ry, rz), 
       type = type, 
       id = as.character(id), 
       description = as.character(desc))
}

Set up a toy example

If you already have a set of x, y, z coordinates with id's you can skip this.

n <- 10
cx <- voxelCoordinates[1]
cy <- voxelCoordinates[2]
cz <- voxelCoordinates[3]
r <- 5 * voxelSize[3]

th <- seq(0,2*pi, length = n)
toy <- cbind(x = r * cos(th) + cx, y = r * sin(th) + cy, z = cz, id = 1:n)

Edit the state list

Using this example you'll need to have your x, y, z and id variables in a matrix or data.frame -- mine is called toy.

dat <- apply(toy, 1, as.list)
out <- lapply(dat, function(x) do.call(makeEllipse,x))

## store our annotations in the new layer list
MyAnnotations$annotations <-  out

## add our new layer to the state
h$layers$MyAnnotations <- MyAnnotations

Write to file

myFile <- file("MyAnnotationState.json", "w")
writeLines(rjson::toJSON(h, indent = 2), myFile) 
close(myFile)

Now you can replace the JSON state in your neuroglancer window with the contents of your new JSON file MyAnnotationStats.json.

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