diff --git a/DESCRIPTION b/DESCRIPTION
index 20c0170..129fb66 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RCon3D
 Title: Analysis of Confocal Images of Microbial Biofilms
-Version: 1.2.5
+Version: 1.2.6
 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre"))
 Description: Various 3D analyses of confocal images. E.g. Quantification, co-aggregation and identifying 3D aggregates.
 Depends: R (>= 3.2.5)
@@ -21,4 +21,4 @@ Suggests:
 License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.1
diff --git a/R/quant.R b/R/quant.R
index f57fd0c..02f6b3c 100644
--- a/R/quant.R
+++ b/R/quant.R
@@ -1,16 +1,17 @@
 #' Quantifies the pixels in images
 #'
-#' Quantifies the number of pixels for each channel in each layer (z-stack)
+#' Quantifies the number of pixels for each channel in any direction (default z-stack)
 #' @param imgs The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.
 #' @param channels Character vector with name(s) of channels. Channel names should be in the names of the array files
 #' @param naming Optional. Add metadata to the output dataframe by looking through names of array files. Should be a list of character vectors, each list element will be added as a variable. Example: naming=list(Time=c("T0","T1","T2")). The function inserts a variable called Time, and then looks through the names of the array files and inserts characters mathcing either T0, T1 or T2
 #' @param cores Number of cores for parallel computing
+#' @param axis Axis to aggregate over (1: x, 2: y, 3:z). Default 3 (z-axis)
 #' @keywords array image quantify
 #' @return A dataframe with number of pixels for each layer
 #' @import foreach doSNOW
 #' @export
 
-quant <- function(imgs,channels,naming = NULL,cores = 1) {
+quant <- function(imgs,channels,naming = NULL,cores = 1,axis=3) {
   
   # Loop for each channel
   qua.fin <- list()
@@ -41,7 +42,7 @@ quant <- function(imgs,channels,naming = NULL,cores = 1) {
       ch_t <- readRDS(ch_files[k])
       
       # Count for each layer
-      q <- apply(ch_t, 3, sum)
+      q <- apply(ch_t, axis, sum)
       
       # Output
       temp <- cbind(sub(paste0("_Array.*"),"",sub(".*/", "", ch_files[k])),channels[z],q,1:length(q))
diff --git a/man/clumps.Rd b/man/clumps.Rd
index 840dd50..bbcd6e9 100644
--- a/man/clumps.Rd
+++ b/man/clumps.Rd
@@ -4,10 +4,22 @@
 \alias{clumps}
 \title{Find 3D aggregates/clumps}
 \usage{
-clumps(imgs, channels, kern.neighbour = c(3, 3, 3),
-  type.neighbour = "box", kern.smooth = NULL, type.smooth = "box",
-  layers = NULL, pwidth = NULL, zstep = NULL, naming = NULL,
-  coords = FALSE, thresh = 0, points = NULL, cores = 1)
+clumps(
+  imgs,
+  channels,
+  kern.neighbour = c(3, 3, 3),
+  type.neighbour = "box",
+  kern.smooth = NULL,
+  type.smooth = "box",
+  layers = NULL,
+  pwidth = NULL,
+  zstep = NULL,
+  naming = NULL,
+  coords = FALSE,
+  thresh = 0,
+  points = NULL,
+  cores = 1
+)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/clumps_dist.Rd b/man/clumps_dist.Rd
index 7c0761d..d7965a5 100644
--- a/man/clumps_dist.Rd
+++ b/man/clumps_dist.Rd
@@ -4,8 +4,7 @@
 \alias{clumps_dist}
 \title{Find distances between 3D aggregates/clumps}
 \usage{
-clumps_dist(clumps.x, clumps.y = clumps.x, pwidth = 1, zstep = 1,
-  cores = 1)
+clumps_dist(clumps.x, clumps.y = clumps.x, pwidth = 1, zstep = 1, cores = 1)
 }
 \arguments{
 \item{clumps.x}{Data.frame output from the \code{clumps} function (...$Aggregates)}
diff --git a/man/clumps_plot.Rd b/man/clumps_plot.Rd
index fc34ee2..3a71981 100644
--- a/man/clumps_plot.Rd
+++ b/man/clumps_plot.Rd
@@ -4,9 +4,17 @@
 \alias{clumps_plot}
 \title{Plot 3D aggregates}
 \usage{
-clumps_plot(clumps.out, replica = 1, col = "agg", pwidth = NULL,
-  zstep = NULL, center = NULL, radius = NULL, thresh = 0,
-  thresh.m = FALSE)
+clumps_plot(
+  clumps.out,
+  replica = 1,
+  col = "agg",
+  pwidth = NULL,
+  zstep = NULL,
+  center = NULL,
+  radius = NULL,
+  thresh = 0,
+  thresh.m = FALSE
+)
 }
 \arguments{
 \item{clumps.out}{Output from \code{clumps}}
diff --git a/man/co_agg.Rd b/man/co_agg.Rd
index 48f4692..ddf94f2 100644
--- a/man/co_agg.Rd
+++ b/man/co_agg.Rd
@@ -5,11 +5,34 @@
 \alias{co_agg.default}
 \title{3D co-aggregation}
 \usage{
-co_agg(imgs, channels, size, npixel, R = 10, dstep = 1, pwidth, zstep,
-  cores = 1, kern.smooth = NULL, layers = NULL, naming = NULL)
+co_agg(
+  imgs,
+  channels,
+  size,
+  npixel,
+  R = 10,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 
-co_agg.default(imgs, channels, size, npixel, dstep = 1, pwidth, zstep,
-  cores = 1, kern.smooth = NULL, layers = NULL, naming = NULL)
+co_agg.default(
+  imgs,
+  channels,
+  size,
+  npixel,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/cross_ratio.Rd b/man/cross_ratio.Rd
index 8678aff..f9070f4 100644
--- a/man/cross_ratio.Rd
+++ b/man/cross_ratio.Rd
@@ -5,13 +5,36 @@
 \alias{cross_ratio.default}
 \title{3D cross-ratio}
 \usage{
-cross_ratio(imgs, focal.channel, target.channels, size, npixel, R = 10,
-  dstep = 1, pwidth, zstep, cores = 1, kern.smooth = NULL,
-  layers = NULL, naming = NULL)
+cross_ratio(
+  imgs,
+  focal.channel,
+  target.channels,
+  size,
+  npixel,
+  R = 10,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 
-cross_ratio.default(imgs, focal.channel, target.channels, size, npixel,
-  dstep = 1, pwidth, zstep, cores = 1, kern.smooth = NULL,
-  layers = NULL, naming = NULL)
+cross_ratio.default(
+  imgs,
+  focal.channel,
+  target.channels,
+  size,
+  npixel,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/layer_split.Rd b/man/layer_split.Rd
index 44dbaeb..36ecff8 100644
--- a/man/layer_split.Rd
+++ b/man/layer_split.Rd
@@ -4,8 +4,17 @@
 \alias{layer_split}
 \title{Split quantification in Top, Middle and Bottom}
 \usage{
-layer_split(qua, side.x, side.y, pt, add.t, add.b, channel = NULL,
-  trim = FALSE, layer.start = NULL)
+layer_split(
+  qua,
+  side.x,
+  side.y,
+  pt,
+  add.t,
+  add.b,
+  channel = NULL,
+  trim = FALSE,
+  layer.start = NULL
+)
 }
 \arguments{
 \item{qua}{A dataframe from the \code{quant} function}
diff --git a/man/loadIMG.Rd b/man/loadIMG.Rd
index c91b136..c510ca4 100644
--- a/man/loadIMG.Rd
+++ b/man/loadIMG.Rd
@@ -4,8 +4,7 @@
 \alias{loadIMG}
 \title{Load .tif images into R}
 \usage{
-loadIMG(path, channels, split = FALSE, multi = NULL,
-  multi.name = NULL)
+loadIMG(path, channels, split = FALSE, multi = NULL, multi.name = NULL)
 }
 \arguments{
 \item{path}{The path of either a folder with all .tif files to be loaded (if split=FALSE), or a folder where each image is in a separate subfolder with all z-stacks and channels in that folder (if split=TRUE)}
diff --git a/man/morphIMG.Rd b/man/morphIMG.Rd
index 9c4b8d7..1b781fd 100644
--- a/man/morphIMG.Rd
+++ b/man/morphIMG.Rd
@@ -4,8 +4,7 @@
 \alias{morphIMG}
 \title{Apply mathematical morphology kernel on image and save as RDS}
 \usage{
-morphIMG(imgs, morph = NULL, kern = c(3, 3, 3), type = "box",
-  cores = 1)
+morphIMG(imgs, morph = NULL, kern = c(3, 3, 3), type = "box", cores = 1)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/occupancy.Rd b/man/occupancy.Rd
index 23544a0..622e567 100644
--- a/man/occupancy.Rd
+++ b/man/occupancy.Rd
@@ -5,13 +5,36 @@
 \alias{occupancy.default}
 \title{3D Occupancy}
 \usage{
-occupancy(imgs, focal.channel, target.channel, size, npixel, R = 10,
-  dstep = 1, pwidth, zstep, cores = 1, kern.smooth = NULL,
-  layers = NULL, naming = NULL)
+occupancy(
+  imgs,
+  focal.channel,
+  target.channel,
+  size,
+  npixel,
+  R = 10,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 
-occupancy.default(imgs, focal.channel, target.channel, size, npixel,
-  dstep = 1, pwidth, zstep, cores = 1, kern.smooth = NULL,
-  layers = NULL, naming = NULL)
+occupancy.default(
+  imgs,
+  focal.channel,
+  target.channel,
+  size,
+  npixel,
+  dstep = 1,
+  pwidth,
+  zstep,
+  cores = 1,
+  kern.smooth = NULL,
+  layers = NULL,
+  naming = NULL
+)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/quant.Rd b/man/quant.Rd
index 581fec3..de17c41 100644
--- a/man/quant.Rd
+++ b/man/quant.Rd
@@ -4,7 +4,7 @@
 \alias{quant}
 \title{Quantifies the pixels in images}
 \usage{
-quant(imgs, channels, naming = NULL, cores = 1)
+quant(imgs, channels, naming = NULL, cores = 1, axis = 3)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
@@ -14,12 +14,14 @@ quant(imgs, channels, naming = NULL, cores = 1)
 \item{naming}{Optional. Add metadata to the output dataframe by looking through names of array files. Should be a list of character vectors, each list element will be added as a variable. Example: naming=list(Time=c("T0","T1","T2")). The function inserts a variable called Time, and then looks through the names of the array files and inserts characters mathcing either T0, T1 or T2}
 
 \item{cores}{Number of cores for parallel computing}
+
+\item{axis}{Axis to aggregate over (1: x, 2: y, 3:z). Default 3 (z-axis)}
 }
 \value{
 A dataframe with number of pixels for each layer
 }
 \description{
-Quantifies the number of pixels for each channel in each layer (z-stack)
+Quantifies the number of pixels for each channel in any direction (default z-stack)
 }
 \keyword{array}
 \keyword{image}
diff --git a/man/smoothIMG.Rd b/man/smoothIMG.Rd
index 6f95648..bda833f 100644
--- a/man/smoothIMG.Rd
+++ b/man/smoothIMG.Rd
@@ -4,8 +4,7 @@
 \alias{smoothIMG}
 \title{Median smooth image and save as RDS}
 \usage{
-smoothIMG(imgs, kern.smooth = c(3, 3, 3), type.smooth = "box",
-  cores = 1)
+smoothIMG(imgs, kern.smooth = c(3, 3, 3), type.smooth = "box", cores = 1)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/threshIMG.Rd b/man/threshIMG.Rd
index 1778eb3..7fff3e3 100644
--- a/man/threshIMG.Rd
+++ b/man/threshIMG.Rd
@@ -4,10 +4,16 @@
 \alias{threshIMG}
 \title{Apply thresholding on image and save as RDS}
 \usage{
-threshIMG(imgs, method = "Manual", cores = 1, breaks = 100,
-  opt = 0.1, thresh = rep(0, length(imgs)), BEM.opt = list(start =
-  list(a = -1e+06, b = 0.1, c = 1e+06), control = nls.lm.control(maxiter =
-  1000)))
+threshIMG(
+  imgs,
+  method = "Manual",
+  cores = 1,
+  breaks = 100,
+  opt = 0.1,
+  thresh = rep(0, length(imgs)),
+  BEM.opt = list(start = list(a = -1e+06, b = 0.1, c = 1e+06), control =
+    nls.lm.control(maxiter = 1000))
+)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}
diff --git a/man/xy_splits.Rd b/man/xy_splits.Rd
index 0b1dc9c..d714cdb 100644
--- a/man/xy_splits.Rd
+++ b/man/xy_splits.Rd
@@ -4,8 +4,7 @@
 \alias{xy_splits}
 \title{Analyses for each xy position}
 \usage{
-xy_splits(imgs, channels, do, upper.part = 0.5, layer.start = NULL,
-  cores = 1)
+xy_splits(imgs, channels, do, upper.part = 0.5, layer.start = NULL, cores = 1)
 }
 \arguments{
 \item{imgs}{The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.}