diff --git a/NAMESPACE b/NAMESPACE
index 7b15161..ce5c7c6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(banc_add_synapses,default)
+S3method(banc_add_synapses,neuron)
+S3method(banc_add_synapses,neuronlist)
 S3method(banc_decapitate,"NULL")
 S3method(banc_decapitate,data.frame)
 S3method(banc_decapitate,hxsurf)
@@ -21,6 +24,7 @@ S3method(geom_neuron,neuronlist)
 S3method(ggplot2_neuron_path,mesh3d)
 S3method(ggplot2_neuron_path,neuron)
 S3method(ggplot2_neuron_path,neuronlist)
+export(banc_add_synapses)
 export(banc_all_synapses)
 export(banc_backbone_proofread)
 export(banc_brain_side_view)
@@ -43,6 +47,7 @@ export(banc_neuron_comparison_plot)
 export(banc_nm2raw)
 export(banc_nuclei)
 export(banc_partner_summary)
+export(banc_partners)
 export(banc_peripheral_nerves)
 export(banc_raw2nm)
 export(banc_read_l2dp)
diff --git a/R/banc-table.R b/R/banc-table.R
index cf963c3..8dd788a 100644
--- a/R/banc-table.R
+++ b/R/banc-table.R
@@ -120,7 +120,7 @@ banctable_set_token <- function(user, pwd, url = "https://cloud.seatable.io/"){
                             password = pwd, server_url = url)
   ac$auth()
   Sys.setenv(banctable_TOKEN = ac$token)
-  cat("banctable_TOKEN='", ac$token, "'\n", sep = "", append = TRUE,
+  cat("BANCTABLE_TOKEN='", ac$token, "'\n", sep = "", append = TRUE,
       file = path.expand("~/.Renviron"))
   return(invisible(NULL))
 }
diff --git a/R/ggplot2.R b/R/ggplot2.R
index 7b69f66..1168ca1 100644
--- a/R/ggplot2.R
+++ b/R/ggplot2.R
@@ -528,6 +528,167 @@ geom_neuron.dotprops <- function(x = NULL, rotation_matrix = NULL, root = 3, col
                      ...)
 }
 
+#' @rdname geom_neuron
+#' @method geom_neuron synapticneuron
+#' @export
+geom_neuron.synapticneuron <- function(x = NULL,
+                                       rotation_matrix = NULL,
+                                       root = 3,
+                                       cols = c("navy", "turquoise"),
+                                       stat = "identity", position = "identity",
+                                       na.rm = FALSE,
+                                       show.legend = NA,
+                                       inherit.aes = FALSE,
+                                       ...) {
+  if("splitneuron"%in%class(x)){
+    geomneuron<-geom_neuron.splitneuron(x = x,
+                                   rotation_matrix = rotation_matrix,
+                                   root = root,
+                                   cols = cols,
+                                   stat = stat,
+                                   position = position,
+                                   na.rm = na.rm,
+                                   show.legend = show.legend,
+                                   inherit.aes = inherit.aes,
+                                   ...)
+  }else{
+    geomneuron<-geom_neuron.neuron(x = x,
+                                   rotation_matrix = rotation_matrix,
+                                   root = root,
+                                   cols = cols,
+                                   stat = stat,
+                                   position = position,
+                                   na.rm = na.rm,
+                                   show.legend = show.legend,
+                                   inherit.aes = inherit.aes,
+                                   ...)
+  }
+  if(!is.null(x$connectors)){
+    syns.in <- nat::xyzmatrix(subset(x$connectors, x$connectors$prepost==1))
+    syns.out <- nat::xyzmatrix(subset(x$connectors, x$connectors$prepost==0))
+    if(!is.null(rotation_matrix)){
+      syns.in <- as.data.frame(t(rotation_matrix[,1:3] %*% t(syns.in)))
+      syns.in <- syns.in[,-4]
+      colnames(syns.in) <- c("X","Y","Z")
+      syns.out <- as.data.frame(t(rotation_matrix[,1:3] %*% t(syns.out)))
+      syns.out <- syns.out[,-4]
+      colnames(syns.out) <- c("X","Y","Z")
+    }
+    glist <- list(
+      ggplot2::geom_point(data = syns.in,
+                          mapping = ggplot2::aes(x = .data$X,
+                                                 y = .data$Y),
+                          color = "#132157",
+                          size = root/50,
+                          alpha = 0.5),
+      ggplot2::geom_point(data = syns.out,
+                          mapping = ggplot2::aes(x = .data$X,
+                                                 y = .data$Y),
+                          color = "#D72000",
+                          size = root/50,
+                          alpha = 0.5)
+    )
+    c(geomneuron,glist)
+  }else{
+    geomneuron
+  }
+}
+
+#' @rdname geom_neuron
+#' @method geom_neuron dotprops
+#' @export
+geom_neuron.splitneuron <- function(x = NULL,
+                                   rotation_matrix = NULL,
+                                   root = 3,
+                                   cols = c("navy", "turquoise"),
+                                   stat = "identity", position = "identity",
+                                   na.rm = FALSE,
+                                   show.legend = NA,
+                                   inherit.aes = FALSE,
+                                   ...) {
+
+  # Get parts
+  if(root){
+    x$tags$soma <- nat::rootpoints(x)
+  }
+  soma <- catmaid::soma(x)
+  if(!is.null(rotation_matrix)){
+    soma <- as.data.frame(t(rotation_matrix[,1:3] %*% t(nat::xyzmatrix(soma))))
+    soma <- soma[,-4]
+    colnames(soma) <- c("X","Y","Z")
+  }
+  dendrites.v = subset(rownames(x$d), x$d$Label == 3)
+  axon.v = subset(rownames(x$d), x$d$Label == 2)
+  p.d.v = subset(rownames(x$d), x$d$Label == 4)
+  p.n.v = subset(rownames(x$d), x$d$Label == 7)
+  null.v = subset(rownames(x$d), x$d$Label ==  0 | is.na(x$d$Label))
+
+  # Get cable
+  dendrites = tryCatch(nat::prune_vertices(x,
+                                           verticestoprune = as.integer(c(axon.v,p.d.v, p.n.v, null.v))),
+                       error = function(e) NULL)
+  axon = tryCatch(nat::prune_vertices(x,
+                                      verticestoprune = as.integer(c(dendrites.v, p.d.v, p.n.v, null.v))),
+                  error = function(e) NULL)
+  p.d = tryCatch(nat::prune_vertices(x, verticestoprune = as.integer(c(axon.v, dendrites.v, p.n.v, null.v))),
+                 error = function(e) NULL)
+  p.n = tryCatch(nat::prune_vertices(x, verticestoprune = as.integer(c(axon.v, dendrites.v, p.d.v, null.v))),
+                 error = function(e) NULL)
+  nulls = tryCatch(nat::prune_vertices(x, verticestoprune = as.integer(c(axon.v, dendrites.v, p.d.v, p.n.v))),
+                 error = function(e) NULL)
+
+  # Make ggplot2 objects
+  g.dendrites <- ggplot2_neuron_path.neuron(dendrites, rotation_matrix = rotation_matrix)
+  g.axon <- ggplot2_neuron_path.neuron(axon, rotation_matrix = rotation_matrix)
+  g.p.d <- ggplot2_neuron_path.neuron(p.d, rotation_matrix = rotation_matrix)
+  g.p.n <- ggplot2_neuron_path.neuron(p.n, rotation_matrix = rotation_matrix)
+  g.nulls <- ggplot2_neuron_path.neuron(nulls, rotation_matrix = rotation_matrix)
+
+  # Make geom objects
+  list(
+    ggplot2::geom_path(mapping = ggplot2::aes(x = .data$X, y = .data$Y, group = .data$group),
+                       data = g.dendrites, col = "#54BCD1",
+                       stat = stat, position = position, na.rm = na.rm,
+                       show.legend = show.legend, inherit.aes = inherit.aes, alpha = 1),
+    ggplot2::geom_path(mapping = ggplot2::aes(x = .data$X, y = .data$Y, group = .data$group),
+                       data = g.axon, col = "#EF7C12",
+                       stat = stat, position = position, na.rm = na.rm,
+                       show.legend = show.legend, inherit.aes = inherit.aes,  alpha = 1),
+    ggplot2::geom_path(mapping = ggplot2::aes(x = .data$X, y = .data$Y, group = .data$group),
+                       data = g.p.d, col = "#8FDA04",
+                       stat = stat, position = position, na.rm = na.rm,
+                       show.legend = show.legend, inherit.aes = inherit.aes,  alpha = 1),
+    ggplot2::geom_path(mapping = ggplot2::aes(x = .data$X, y = .data$Y, group = .data$group),
+                       data = g.p.n, col = "#C70E7B",
+                       stat = stat, position = position, na.rm = na.rm,
+                       show.legend = show.legend, inherit.aes = inherit.aes,  alpha = 1),
+    ggplot2::geom_path(mapping = ggplot2::aes(x = .data$X, y = .data$Y, group = .data$group),
+                       data = g.nulls, col = "#B3B3B3",
+                       stat = stat, position = position, na.rm = na.rm,
+                       show.legend = show.legend, inherit.aes = inherit.aes,  alpha = 1),
+    ggplot2::geom_point(mapping = ggplot2::aes(x = .data$X, y = .data$Y),
+                        data = soma, col = "black",
+                        color = cols[1], alpha = 0.75, size = root)
+    )
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 #' Create a ggplot2 Visualisation of Neuron Objects
 #'
 #' @description
diff --git a/R/l2.R b/R/l2.R
index 15f1410..c318167 100644
--- a/R/l2.R
+++ b/R/l2.R
@@ -95,6 +95,8 @@ banc_read_l2skel <- function(id, OmitFailures=TRUE, dataset=NULL, ...) {
 #' obtained using `bancr::banc_nuclei()`. This data frame is assumed to have
 #' columns named `root_id` and `nucleus_position_nm`, where `nucleus_position_nm`
 #' specifies the 3D coordinates of the soma for each `root_id`.
+#' @param estimate if \code{TRUE} and nucleus position is not in `banc_nuclei`,
+#' then root is estimated as a leaf node furthest outside of the brain neuropil.
 #' @param ... Methods passed to \code{nat::nlapply}.
 #'
 #' @return The function returns the re-rooted `neuron` object.
@@ -107,12 +109,12 @@ banc_read_l2skel <- function(id, OmitFailures=TRUE, dataset=NULL, ...) {
 #' }
 #' @export
 #' @rdname banc_reroot
-banc_reroot <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...) UseMethod("banc_reroot")
+banc_reroot <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), estimate = TRUE, ...) UseMethod("banc_reroot")
 
 #' @rdname banc_reroot
 #' @method banc_reroot neuron
 #' @export
-banc_reroot.neuron <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...){
+banc_reroot.neuron <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), estimate = TRUE, ...){
   if(is.null(id)){
     id <- x$root_id
   }
@@ -124,7 +126,7 @@ banc_reroot.neuron <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(),
     soma <- nat::xyzmatrix(df$nucleus_position_nm)[1,]
     x <- nat::reroot(x = x, point = c(soma))
     x$tags$soma <- nat::rootpoints(x )
-  }else{ # As best we can
+  }else if (estimate){ # As best we can
     warning(sprintf("no valid nucleus ID detecting for %s, estimating root point"),id)
     leaves <- nat::endpoints(x)
     npoints1 <- nat::xyzmatrix(x)[leaves,]
@@ -142,6 +144,8 @@ banc_reroot.neuron <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(),
                                        nat::xyzmatrix(bancr::banc_neck_connective.surf)), k = 1)
     soma <-nat::xyzmatrix(npoints)[which.max(nearest$nn.dists),]
     x <- nat::reroot(x = x, point = c(soma))
+  }else{
+    warning(sprintf("no valid nucleus ID detecting for %s, no action taken"),id)
   }
   x
 }
@@ -149,7 +153,7 @@ banc_reroot.neuron <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(),
 #' @rdname banc_reroot
 #' @method banc_reroot neuronlist
 #' @export
-banc_reroot.neuronlist <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...){
+banc_reroot.neuronlist <- function(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), estimate = TRUE, ...){
   if(is.null(id)){
     id <- names(x)
   }
diff --git a/R/partners.R b/R/partners.R
index a76df47..5f61605 100644
--- a/R/partners.R
+++ b/R/partners.R
@@ -28,6 +28,7 @@
 #'   slice_max(weight, n = 20) %>%
 #'   banc_scene(open=TRUE)
 #' }
+#' @rdname banc_partners
 banc_partner_summary <- function(rootids,
                                  partners = c("outputs", "inputs"),
                                  threshold = 0,
@@ -87,6 +88,8 @@ banc_datastack_name <- memoise::memoise(function() {
 #' fpo=banc_partners(banc_latestid("720575941478275714"), partners='out')
 #' points3d(banc_raw2nm(fpo$pre_pt_position), col='red')
 #' }
+#' @export
+#' @rdname banc_partners
 banc_partners <- function(rootids, partners=c("input", "output"), ...) {
   partners=match.arg(partners)
   rootids=banc_ids(rootids)
diff --git a/R/synapses.R b/R/synapses.R
index f62ae9f..7ac86e5 100644
--- a/R/synapses.R
+++ b/R/synapses.R
@@ -127,3 +127,134 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
   # path <- 'gs://zetta_lee_fly_cns_001_synapse/240529_run/240604_assignment/final_edgelist.df'
   # df <- googleCloudStorageR::gcs_get_object(path, parseFunction = function(x) read.csv(x, nrows = 1000))
 # }
+
+
+#' Add synapses to neuron objects
+#'
+#' This function family adds synaptic data to neuron objects or neuron lists.
+#' It retrieves synaptic connections and attaches them to the neuron object(s).
+#'
+#' @param x A neuron object, neuronlist, or other object to add synapses to
+#' @param id The root ID of the neuron. If NULL, it uses the ID from the neuron object
+#' @param connectors A dataframe of synaptic connections. If NULL, it retrieves the data
+#' @param size.threshold Minimum size threshold for synapses to include
+#' @param remove.autapses Whether to remove autapses (self-connections)
+#' @param ... Additional arguments passed to methods, \code{nat::nlapply}
+#'
+#' @return An object of the same type as `x`, with synapses added
+#'
+#' @export
+banc_add_synapses <- function(x, ...) {
+  UseMethod("banc_add_synapses")
+}
+
+#' @rdname banc_add_synapses
+#' @export
+banc_add_synapses.neuron <- function(x,
+                              id = NULL,
+                              connectors = NULL,
+                              size.threshold = 5,
+                              remove.autapses = TRUE,
+                              ...){
+  # Get valid root id
+  if(is.null(id)){
+    id <- x$id
+  }
+
+  # Get synaptic data
+  if(is.null(connectors)){
+    connectors.in <- bancr:::banc_partners(id, partners = "input")
+    if(nrow(connectors.in)){
+      connectors.in.xyz <- do.call(rbind,connectors.in$post_pt_position)
+      connectors.in.xyz <- as.data.frame(connectors.in.xyz)
+      colnames(connectors.in.xyz) <- c("X","Y","Z")
+      connectors.in <- cbind(connectors.in,connectors.in.xyz)
+      connectors.in <- connectors.in %>%
+        dplyr::rename(connector_id = id,
+                      pre_id = pre_pt_root_id,
+                      pre_svid = pre_pt_supervoxel_id,
+                      post_id = post_pt_root_id,
+                      post_svid = post_pt_supervoxel_id) %>%
+        dplyr::filter(size>size.threshold) %>%
+        dplyr::mutate(prepost = 1) %>%
+        dplyr::select(connector_id, pre_id, post_id, prepost, pre_svid, post_svid, size, X, Y, Z)
+    }
+    connectors.out <- bancr:::banc_partners(id, partners = "output")
+    if(nrow(connectors.out)){
+      connectors.out.xyz <- do.call(rbind,connectors.out$pre_pt_position)
+      connectors.out.xyz <- as.data.frame(connectors.out.xyz)
+      colnames(connectors.out.xyz) <- c("X","Y","Z")
+      connectors.out <- cbind(connectors.out,connectors.out.xyz)
+      connectors.out <- connectors.out %>%
+        dplyr::rename(connector_id = id,
+                      pre_id = pre_pt_root_id,
+                      pre_svid = pre_pt_supervoxel_id,
+                      post_id = post_pt_root_id,
+                      post_svid = post_pt_supervoxel_id) %>%
+        dplyr::filter(size>size.threshold) %>%
+        dplyr::mutate(prepost = 0) %>%
+        dplyr::select(connector_id, pre_id, post_id, prepost, pre_svid, post_svid, size, X, Y, Z)
+    }
+    connectors <- rbind(connectors.in,connectors.out)
+  }else{
+    connectors <- connectors %>%
+      dplyr::filter(post_id==id|pre_id==id)
+  }
+  if(remove.autapses) {
+    connectors=connectors[connectors$post_id!=connectors$pre_id,,drop=FALSE]
+  }
+
+  # Attach synapses
+  if(nrow(connectors)){
+    near <- nabor::knn(query = nat::xyzmatrix(connectors),
+                       data = nat::xyzmatrix(x$d),k=1)
+    connectors$treenode_id <- x$d[near$nn.idx,"PointNo"]
+    x$connectors = as.data.frame(connectors, stringsAsFactors = FALSE)
+  }
+  x$connectors <- connectors
+
+  # Change class to work with connectivity functions in other packages
+  class(x) <- union(c("synapticneuron"), class(x))
+
+  # Return
+  x
+}
+
+#' @rdname banc_add_synapses
+#' @export
+banc_add_synapses.neuronlist <- function(x,
+                                         id = NULL,
+                                         connectors = NULL,
+                                         size.threshold = 5,
+                                         remove.autapses = TRUE,
+                                         ...) {
+  if(is.null(id)){
+    is <- names(x)
+  }
+  nat::nlapply(x,banc_add_synapses.neuron,
+               id=id,
+               connectors=connectors,
+               size.threshold=size.threshold,
+               remove.autapses=remove.autapses)
+}
+
+#' @rdname banc_add_synapses
+#' @export
+banc_add_synapses.default <- function(x,
+                                      id = NULL,
+                                      connectors = NULL,
+                                      size.threshold = 5,
+                                      remove.autapses = TRUE,
+                                      ...) {
+  stop("No method for class ", class(x))
+}
+
+
+
+
+
+
+
+
+
+
diff --git a/R/urls.R b/R/urls.R
index 52cb7eb..9cba020 100644
--- a/R/urls.R
+++ b/R/urls.R
@@ -22,7 +22,7 @@ banc_scene <- function(ids=NULL, open=FALSE) {
   url="https://spelunker.cave-explorer.org/#!middleauth+https://global.daf-apis.com/nglstate/api/v1/6283844278812672"
   url=sub("#!middleauth+", "?", url, fixed = T)
   parts=unlist(strsplit(url, "?", fixed = T))
-  json=try(flywire_fetch(parts[2], token=banc_token(), return = 'text', cache = TRUE))
+  json=try(fafbseg::flywire_fetch(parts[2], token=banc_token(), return = 'text', cache = TRUE))
   if(inherits(json, 'try-error')) {
     badtoken=paste0("You have a token but it doesn't seem to be authorised for banc.\n",
                     "Have you definitely used `banc_set_token()` to make a token for the banc dataset?")
diff --git a/man/banc_add_synapses.Rd b/man/banc_add_synapses.Rd
new file mode 100644
index 0000000..d4946a1
--- /dev/null
+++ b/man/banc_add_synapses.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/synapses.R
+\name{banc_add_synapses}
+\alias{banc_add_synapses}
+\alias{banc_add_synapses.neuron}
+\alias{banc_add_synapses.neuronlist}
+\alias{banc_add_synapses.default}
+\title{Add synapses to neuron objects}
+\usage{
+banc_add_synapses(x, ...)
+
+\method{banc_add_synapses}{neuron}(
+  x,
+  id = NULL,
+  connectors = NULL,
+  size.threshold = 5,
+  remove.autapses = TRUE,
+  ...
+)
+
+\method{banc_add_synapses}{neuronlist}(
+  x,
+  ids = NULL,
+  connectors = NULL,
+  size.threshold = 5,
+  remove.autapses = TRUE,
+  ...
+)
+
+\method{banc_add_synapses}{default}(
+  x,
+  ids = NULL,
+  connectors = NULL,
+  size.threshold = 5,
+  remove.autapses = TRUE,
+  ...
+)
+}
+\arguments{
+\item{x}{A neuron object, neuronlist, or other object to add synapses to}
+
+\item{...}{Additional arguments passed to methods}
+
+\item{id}{The root ID of the neuron. If NULL, it uses the ID from the neuron object}
+
+\item{connectors}{A dataframe of synaptic connections. If NULL, it retrieves the data}
+
+\item{size.threshold}{Minimum size threshold for synapses to include}
+
+\item{remove.autapses}{Whether to remove autapses (self-connections)}
+}
+\value{
+An object of the same type as \code{x}, with synapses added
+}
+\description{
+This function family adds synaptic data to neuron objects or neuron lists.
+It retrieves synaptic connections and attaches them to the neuron object(s).
+}
diff --git a/man/banc_partner_summary.Rd b/man/banc_partners.Rd
similarity index 72%
rename from man/banc_partner_summary.Rd
rename to man/banc_partners.Rd
index 7658c30..0a38586 100644
--- a/man/banc_partner_summary.Rd
+++ b/man/banc_partners.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/partners.R
 \name{banc_partner_summary}
 \alias{banc_partner_summary}
-\alias{banc_partners}
 \title{Summarise the connectivity of banc neurons}
 \usage{
 banc_partner_summary(
@@ -14,8 +13,6 @@ banc_partner_summary(
   datastack_name = NULL,
   ...
 )
-
-banc_partners(rootids, partners = c("input", "output"), ...)
 }
 \arguments{
 \item{rootids}{Character vector specifying one or more BANC rootids. As a
@@ -43,8 +40,7 @@ sensible default is chosen.}
 a data.frame
 }
 \description{
-\code{banc_partners} returns details of each unitary synaptic
-connection (including its xyz location).
+Summarise the connectivity of banc neurons
 }
 \details{
 note that the rootids you pass in must be up to date. See example.
@@ -52,26 +48,18 @@ note that the rootids you pass in must be up to date. See example.
 \examples{
 \dontrun{
 # NB id must be up to date
-sample_id=banc_latestid("720575941480769421")
+sample_id=banc_latestid("720575941478275714")
 head(banc_partner_summary(sample_id))
 head(banc_partner_summary(sample_id, partners='inputs'))
 # get the latest id for an outdate
-banc_partner_summary(banc_latestid("720575941480769421"))
+banc_partner_summary(banc_latestid("720575941478275714"))
 
 ## open banc/flywire scene containing top partners
 library(dplyr)
-banc_partner_summary(banc_latestid("720575941480769421"), partners='inputs') \%>\%
+banc_partner_summary(banc_latestid("720575941478275714"), partners='inputs') \%>\%
   slice_max(weight, n = 20) \%>\%
   banc_scene(open=TRUE)
 }
-\dontrun{
-# plot input and output synapses of a neuron
-nclear3d()
-fpi=banc_partners(banc_latestid("648518346481082458"), partners='in')
-points3d(banc_raw2nm(fpi$post_pt_position), col='cyan')
-fpo=banc_partners(banc_latestid("648518346481082458"), partners='out')
-points3d(banc_raw2nm(fpo$pre_pt_position), col='red')
-}
 }
 \seealso{
 \code{\link{flywire_partner_summary}}, \code{\link{banc_latestid}}
diff --git a/man/banc_reroot.Rd b/man/banc_reroot.Rd
index f5bd62d..b1a3f0f 100644
--- a/man/banc_reroot.Rd
+++ b/man/banc_reroot.Rd
@@ -6,11 +6,29 @@
 \alias{banc_reroot.neuronlist}
 \title{Re-root BANC neuron skeleton at soma}
 \usage{
-banc_reroot(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...)
+banc_reroot(
+  x,
+  id = NULL,
+  banc_nuclei = bancr::banc_nuclei(),
+  estimate = TRUE,
+  ...
+)
 
-\method{banc_reroot}{neuron}(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...)
+\method{banc_reroot}{neuron}(
+  x,
+  id = NULL,
+  banc_nuclei = bancr::banc_nuclei(),
+  estimate = TRUE,
+  ...
+)
 
-\method{banc_reroot}{neuronlist}(x, id = NULL, banc_nuclei = bancr::banc_nuclei(), ...)
+\method{banc_reroot}{neuronlist}(
+  x,
+  id = NULL,
+  banc_nuclei = bancr::banc_nuclei(),
+  estimate = TRUE,
+  ...
+)
 }
 \arguments{
 \item{x}{A \code{banc.neurite} object representing the neuron skeleton.}
@@ -23,6 +41,9 @@ obtained using \code{bancr::banc_nuclei()}. This data frame is assumed to have
 columns named \code{root_id} and \code{nucleus_position_nm}, where \code{nucleus_position_nm}
 specifies the 3D coordinates of the soma for each \code{root_id}.}
 
+\item{estimate}{if \code{TRUE} and nucleus position is not in \code{banc_nuclei},
+then root is estimated as a leaf node furthest outside of the brain neuropil.}
+
 \item{...}{Methods passed to \code{nat::nlapply}.}
 }
 \value{