From 224eb407448ddba53763fc6e67c74fce7cf72af5 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Fri, 7 Aug 2026 21:52:01 +0200
Subject: [PATCH 1/9] export imagearray

---
 NAMESPACE               |  1 +
 R/AllClasses.R          | 18 +++++++++++++++++
 man/ImageArray-class.Rd | 45 +++++++++++++++++++++++++++++++++++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 man/ImageArray-class.Rd

diff --git a/NAMESPACE b/NAMESPACE
index b8e181f..035aa68 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(ImageArray)
 export(createImageArray)
 export(getImageInfo)
 export(writeImageArray)
+exportClasses(ImageArray)
 exportMethods("[")
 exportMethods("[[")
 exportMethods("[[<-")
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 4ad05c2..c056c0f 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -18,6 +18,24 @@ setClassUnion("matrix_array_Array",
   contains="SimpleList",
   prototype=prototype(elementType="matrix_array_Array"))
 
+#' @title ImageArray class
+#'
+#' @description
+#' An S4 container for a multi-resolution (pyramidal) image, holding the
+#' pyramid levels together with their axis names and scales. Objects are
+#' created with \code{\link{ImageArray}}.
+#'
+#' @slot levels an \code{ImageList} of pyramid levels, ordered from the
+#'   highest to the lowest resolution
+#' @slot axes a character vector of axis names, a subset of
+#'   \code{c("c", "y", "x", "z", "t")}, of the same length as the number of
+#'   dimensions of every level
+#' @slot scales a list of named numeric vectors, one per level, where names
+#'   are a subset of \code{axes} and values are the scales of these axes. See
+#'   \url{https://ngff.openmicroscopy.org/} for more information. 
+#'
+#' @keywords internal
+#' @exportClass ImageArray
 .ImageArray <- setClass(
   Class = "ImageArray",
   slots = c(
diff --git a/man/ImageArray-class.Rd b/man/ImageArray-class.Rd
new file mode 100644
index 0000000..1152515
--- /dev/null
+++ b/man/ImageArray-class.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R, R/ImageArray.R
+\docType{class}
+\name{ImageArray-class}
+\alias{ImageArray-class}
+\alias{.ImageArray}
+\alias{createImageArray}
+\title{ImageArray class}
+\usage{
+createImageArray(
+  image,
+  n.levels = NULL,
+  series = NULL,
+  resolution = NULL,
+  max.pixel.threshold = max.pixel.threshold,
+  engine = "EBImage",
+  verbose = FALSE
+)
+}
+\description{
+An S4 container for a multi-resolution (pyramidal) image, holding the
+pyramid levels together with their axis names and scales. Objects are
+created with \code{\link{ImageArray}}.
+}
+\section{Functions}{
+\itemize{
+\item \code{createImageArray()}: deprecated function
+
+}}
+\section{Slots}{
+
+\describe{
+\item{\code{levels}}{an \code{ImageList} of pyramid levels, ordered from the
+highest to the lowest resolution}
+
+\item{\code{axes}}{a character vector of axis names, a subset of
+\code{c("c", "y", "x", "z", "t")}, of the same length as the number of
+dimensions of every level}
+
+\item{\code{scales}}{a list of named numeric vectors, one per level, where names
+are a subset of \code{axes} and values are the scales of these axes. See
+\url{https://ngff.openmicroscopy.org/} for more information.}
+}}
+
+\keyword{internal}

From 3c722b753efdc4896ccdc4dfe6fe076643150a6e Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Fri, 7 Aug 2026 21:54:05 +0200
Subject: [PATCH 2/9] bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a1c4f12..8881df7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ImageArray
 Type: Package
 Title: A framework for on-disk and in-memory image arrays
-Version: 1.1.6
+Version: 1.1.7
 Authors@R: c(
     person("Artür", "Manukyan", 
 		     role=c("aut", "cre"),

From 0b611f4aefdf0813287a22f6d5c42a5e32e5cd2f Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 21:58:23 +0200
Subject: [PATCH 3/9] remove axes slot

---
 R/AllClasses.R  | 16 +++++++---------
 R/AllGenerics.R |  2 ++
 R/ImageArray.R  | 45 +++++++++++++++++++++++++++++++++++++++------
 R/Validity.R    | 35 ++++++++++++++++++++---------------
 4 files changed, 68 insertions(+), 30 deletions(-)

diff --git a/R/AllClasses.R b/R/AllClasses.R
index c056c0f..75b79bb 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -22,17 +22,16 @@ setClassUnion("matrix_array_Array",
 #'
 #' @description
 #' An S4 container for a multi-resolution (pyramidal) image, holding the
-#' pyramid levels together with their axis names and scales. Objects are
-#' created with \code{\link{ImageArray}}.
+#' pyramid levels together with their scales. Objects are created with
+#' \code{\link{ImageArray}}.
 #'
 #' @slot levels an \code{ImageList} of pyramid levels, ordered from the
 #'   highest to the lowest resolution
-#' @slot axes a character vector of axis names, a subset of
-#'   \code{c("c", "y", "x", "z", "t")}, of the same length as the number of
-#'   dimensions of every level
-#' @slot scales a list of named numeric vectors, one per level, where names
-#'   are a subset of \code{axes} and values are the scales of these axes. See
-#'   \url{https://ngff.openmicroscopy.org/} for more information. 
+#' @slot scales a list of named numeric vectors, one per level, where values
+#'   are the scales of these axes. The names of these vectors define the axes
+#'   of the object, hence they are a subset of \code{c("c", "y", "x", "z", "t")}
+#'   and are shared, in the same order, by all levels. See
+#'   \url{https://ngff.openmicroscopy.org/} for more information.
 #'
 #' @keywords internal
 #' @exportClass ImageArray
@@ -40,7 +39,6 @@ setClassUnion("matrix_array_Array",
   Class = "ImageArray",
   slots = c(
     levels = "ImageList",
-    axes = "character",
     scales = "list"
   )
 )
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 2081109..8e91508 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -6,6 +6,8 @@ NULL
 setGeneric("createImageList", 
            function(image, ...) standardGeneric("createImageList"))
 setGeneric("scales", function(object, ...) standardGeneric("scales"))
+setGeneric("scales<-", 
+           function(object, ..., value) standardGeneric("scales<-"))
 setGeneric("axes", function(object, ...) standardGeneric("axes"))
 setGeneric("axes<-", function(object, ..., value) standardGeneric("axes<-"))
 setGeneric("read_image", 
diff --git a/R/ImageArray.R b/R/ImageArray.R
index 2c741ed..13bc54b 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -47,6 +47,8 @@
 #' axes<-,ImageArray-method
 #' scales
 #' scales,ImageArray-method
+#' scales<-
+#' scales<-,ImageArray-method
 #' realize
 #' realize,ImageArray-method
 #' as.raster
@@ -185,13 +187,23 @@ setMethod("length", signature = "ImageArray", function(x) length(x@levels))
 
 #' @describeIn ImageArray-methods get axes metadata of the ImageArray object
 #' @exportMethod axes
-setMethod("axes", "ImageArray", function(object) object@axes)
+setMethod("axes", "ImageArray", function(object)
+  .get_axes_from_scales(scales(object)))
 
-#' @describeIn ImageArray-methods get axes metadata of the ImageArray object
+#' @describeIn ImageArray-methods replace axes metadata of the ImageArray
+#' object, the replacement can only be a permutation of the existing axes
 #' @exportMethod axes<-
-setMethod("axes<-", "ImageArray", function(object, ..., value){
-  value <- .check_axes(object[[1]], axes = value)
-  object@axes <- value
+setReplaceMethod("axes", "ImageArray", function(object, ..., value){
+  ax <- axes(object)
+  
+  # check axes, should be a permutation
+  if(!is.character(value) || length(value) != length(ax) ||
+     anyDuplicated(value) || !setequal(value, ax))
+    stop("axes can only be replaced by a permutation of the existing axes: ",
+         paste(ax, collapse = ","), "!")
+
+  # update axes
+  scales(object) <- lapply(scales(object), \(.) .[value])
   object
 })
 
@@ -199,6 +211,28 @@ setMethod("axes<-", "ImageArray", function(object, ..., value){
 #' @exportMethod scales
 setMethod("scales", "ImageArray", function(object) object@scales)
 
+#' @describeIn ImageArray-methods replace scales metadata of the ImageArray
+#' object, each vector should be named by a permutation of the existing axes
+#' @importFrom methods validObject
+#' @exportMethod scales<-
+setReplaceMethod("scales", "ImageArray", function(object, ..., value) {
+  if(!is.list(value)) stop("scales must be a list!")
+
+  # the axes of an ImageArray object can only be permuted, all remaining
+  # checks are done by the validity of the class below
+  ax <- axes(object)
+  for(s in value){
+    if(is.null(names(s)) || length(s) != length(ax) ||
+       anyDuplicated(names(s)) || !setequal(names(s), ax))
+      stop("names of each vector in scales should be a permutation of ",
+           "the existing axes: ", paste(ax, collapse = ","), "!")
+  }
+
+  object@scales <- value
+  methods::validObject(object)
+  object
+})
+
 ####
 # Create/Write ####
 ####
@@ -528,7 +562,6 @@ ImageArray <- function(
   S4Vectors::new2(
     "ImageArray", 
     levels = image$levels,
-    axes = image$axes,
     scales = scales
   )
 }
diff --git a/R/Validity.R b/R/Validity.R
index d8f708d..e252c4a 100644
--- a/R/Validity.R
+++ b/R/Validity.R
@@ -1,32 +1,37 @@
 .validate_ImageArray <- function(object) {
 
+  # check scales vs levels, this is done first since the axes are
+  # given by the names of the scales
+  sc <- scales(object)
+  if (!is.list(sc)) stop("scales must be a list!")
+  if(length(sc) != length(object@levels))
+    stop("scales should be of the same length as levels!")
+
   # check default axes
   ax <- axes(object)
-  if (!all(ax %in% .AXES)) {
-    stop("The axes of the ImageArray object should be a subset of ",  
+  if (!all(ax %in% .AXES))
+    stop("The axes of the ImageArray object should be a subset of ",
          deparse(.AXES))
-  }
-  
-  # check scales
-  sc <- scales(object)
+    
+  # check duplicate axes
+  ind_dup <- which(table(ax) > 1)
+  if (length(ind_dup))
+    stop("Duplicated axes are detected: ",
+         paste(names(ind_dup), collapse = ","))
+
+  # check scales, all levels should carry the same axes in the same order
   for(s in sc){
-    if(!all(names(s) %in% ax)) stop("scale names do not match axes")
-    if(!all(is.numeric(s) & is.finite(s))) 
+    if(!identical(names(s), ax)) stop("scale names do not match axes")
+    if(!all(is.numeric(s) & is.finite(s)))
       stop("scale entries are not numeric")
   }
 
   # check all dim vs axes
   all_length <- vapply(object@levels, function(x) length(dim(x)), integer(1))
-  if (!all(all_length == length(ax))) {
+  if (!all(all_length == length(ax)))
     stop(
       "The number of dimensions of all levels should match the number of axes."
     )
-  }
-  
-  # check all dim vs scales
-  all_dim <- lapply(object@levels, function(x) dim(x))
-  if(length(sc) != length(all_dim))
-    stop("scales should be of the same length as levels!")
 
   TRUE
 }

From 2fd5d481a7bc2b212cc79ae3852908b888c8197e Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 22:27:40 +0200
Subject: [PATCH 4/9] claude review

---
 NAMESPACE                                     |  4 +-
 R/ImageArray.R                                |  6 +-
 man/ImageArray-class.Rd                       | 33 ++-----
 ...mageArray.Rd => ImageArray-constructor.Rd} | 18 +++-
 man/ImageArray-methods.Rd                     | 10 +-
 tests/testthat/test-axes.R                    | 61 ++++++++++++
 tests/testthat/test-scales.R                  | 93 +++++++++++++++++++
 7 files changed, 193 insertions(+), 32 deletions(-)
 rename man/{ImageArray.Rd => ImageArray-constructor.Rd} (86%)

diff --git a/NAMESPACE b/NAMESPACE
index 035aa68..a983ad0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,6 +13,7 @@ exportMethods("[[")
 exportMethods("[[<-")
 exportMethods("axes<-")
 exportMethods("path<-")
+exportMethods("scales<-")
 exportMethods(affine)
 exportMethods(aperm)
 exportMethods(axes)
@@ -76,7 +77,8 @@ importFrom(methods,
   setClassUnion,
   setOldClass,
   slot,
-  slotNames
+  slotNames,
+  validObject
 )
 importFrom(rhdf5,
   h5createFile,
diff --git a/R/ImageArray.R b/R/ImageArray.R
index 13bc54b..5ac8e46 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -486,8 +486,8 @@ setMethod("createImageList", "list", createListFromList)
 #'  typical an integer starting from 1.
 #' @param verbose verbose
 #'
-#' @name ImageArray
-#' @rdname ImageArray
+#' @name ImageArray-constructor
+#' @rdname ImageArray-constructor
 #' 
 #' @aliases 
 #' createImageArray
@@ -566,7 +566,7 @@ ImageArray <- function(
   )
 }
 
-#' @describeIn ImageArray deprecated function
+#' @describeIn ImageArray-constructor deprecated function
 #' @export
 createImageArray <- function(
     image,
diff --git a/man/ImageArray-class.Rd b/man/ImageArray-class.Rd
index 1152515..fb73890 100644
--- a/man/ImageArray-class.Rd
+++ b/man/ImageArray-class.Rd
@@ -1,44 +1,25 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/AllClasses.R, R/ImageArray.R
+% Please edit documentation in R/AllClasses.R
 \docType{class}
 \name{ImageArray-class}
 \alias{ImageArray-class}
 \alias{.ImageArray}
-\alias{createImageArray}
 \title{ImageArray class}
-\usage{
-createImageArray(
-  image,
-  n.levels = NULL,
-  series = NULL,
-  resolution = NULL,
-  max.pixel.threshold = max.pixel.threshold,
-  engine = "EBImage",
-  verbose = FALSE
-)
-}
 \description{
 An S4 container for a multi-resolution (pyramidal) image, holding the
-pyramid levels together with their axis names and scales. Objects are
-created with \code{\link{ImageArray}}.
+pyramid levels together with their scales. Objects are created with
+\code{\link{ImageArray}}.
 }
-\section{Functions}{
-\itemize{
-\item \code{createImageArray()}: deprecated function
-
-}}
 \section{Slots}{
 
 \describe{
 \item{\code{levels}}{an \code{ImageList} of pyramid levels, ordered from the
 highest to the lowest resolution}
 
-\item{\code{axes}}{a character vector of axis names, a subset of
-\code{c("c", "y", "x", "z", "t")}, of the same length as the number of
-dimensions of every level}
-
-\item{\code{scales}}{a list of named numeric vectors, one per level, where names
-are a subset of \code{axes} and values are the scales of these axes. See
+\item{\code{scales}}{a list of named numeric vectors, one per level, where values
+are the scales of these axes. The names of these vectors define the axes
+of the object, hence they are a subset of \code{c("c", "y", "x", "z", "t")}
+and are shared, in the same order, by all levels. See
 \url{https://ngff.openmicroscopy.org/} for more information.}
 }}
 
diff --git a/man/ImageArray.Rd b/man/ImageArray-constructor.Rd
similarity index 86%
rename from man/ImageArray.Rd
rename to man/ImageArray-constructor.Rd
index 888d838..8790ffc 100644
--- a/man/ImageArray.Rd
+++ b/man/ImageArray-constructor.Rd
@@ -1,6 +1,7 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ImageArray.R
-\name{ImageArray}
+\name{ImageArray-constructor}
+\alias{ImageArray-constructor}
 \alias{ImageArray}
 \alias{createImageArray}
 \alias{createImageArray,ImageArray-method}
@@ -17,6 +18,16 @@ ImageArray(
   resolution = NULL,
   verbose = FALSE
 )
+
+createImageArray(
+  image,
+  n.levels = NULL,
+  series = NULL,
+  resolution = NULL,
+  max.pixel.threshold = max.pixel.threshold,
+  engine = "EBImage",
+  verbose = FALSE
+)
 }
 \arguments{
 \item{image}{a path to a file, a single array or a list of arrays
@@ -58,6 +69,11 @@ An ImageArray object
 \description{
 creates an object of ImageArray class
 }
+\section{Functions}{
+\itemize{
+\item \code{createImageArray()}: deprecated function
+
+}}
 \examples{
 # get image
 library(EBImage)
diff --git a/man/ImageArray-methods.Rd b/man/ImageArray-methods.Rd
index 1b520b1..eb3ebd0 100644
--- a/man/ImageArray-methods.Rd
+++ b/man/ImageArray-methods.Rd
@@ -19,6 +19,8 @@
 \alias{axes<-,ImageArray-method}
 \alias{scales}
 \alias{scales,ImageArray-method}
+\alias{scales<-}
+\alias{scales<-,ImageArray-method}
 \alias{realize}
 \alias{realize,ImageArray-method}
 \alias{as.raster}
@@ -54,6 +56,8 @@
 
 \S4method{scales}{ImageArray}(object)
 
+\S4method{scales}{ImageArray}(object, ...) <- value
+
 \S4method{realize}{ImageArray}(x, level = NULL, max.pixel.size = NULL, min.pixel.size = NULL)
 
 \method{as.raster}{ImageArray}(x, level = NULL, max.pixel.size = NULL, min.pixel.size = NULL, ...)
@@ -131,10 +135,14 @@ for \code{ImageArray} objects
 
 \item \code{axes(ImageArray)}: get axes metadata of the ImageArray object
 
-\item \code{axes(ImageArray) <- value}: get axes metadata of the ImageArray object
+\item \code{axes(ImageArray) <- value}: replace axes metadata of the ImageArray
+object, the replacement can only be a permutation of the existing axes
 
 \item \code{scales(ImageArray)}: get scales metadata of the ImageArray object
 
+\item \code{scales(ImageArray) <- value}: replace scales metadata of the ImageArray
+object, each vector should be named by a permutation of the existing axes
+
 \item \code{realize(ImageArray)}: realize the array
 
 \item \code{as.raster(ImageArray)}: create a raster object
diff --git a/tests/testthat/test-axes.R b/tests/testthat/test-axes.R
index 881b60f..92f4700 100644
--- a/tests/testthat/test-axes.R
+++ b/tests/testthat/test-axes.R
@@ -67,6 +67,10 @@ test_that("duplicate axes", {
     axes <- .check_axes(mat3d, c("c", "x", "x")),
     "axes should include at least both x and y dimensions!"
   )
+  expect_error(
+    axes <- .check_axes(mat4d, c("x", "y", "c", "c")),
+    "Duplicated axes are detected: c"
+  )
 })
 
 test_that("get axes from scales", {
@@ -87,4 +91,61 @@ test_that("get axes from scales", {
     .get_axes_from_scales(list(c())),
     "Each vector in scales should be named!"
   )
+})
+
+test_that("get axes of an ImageArray", {
+
+  # the axes of an ImageArray are given by the names of its scales
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+  expect_equal(axes(imgarray), c("c", "y", "x"))
+  expect_equal(axes(imgarray), names(scales(imgarray)[[1]]))
+
+  # axes are also picked up from user provided scales
+  imgarray <- ImageArray(image = list(array(1:25, dim = c(5,5)),
+                                      array(1:9, dim = c(3,3))),
+                         scales = list(c(y = 1, x = 1),
+                                       c(y = 0.6, x = 0.6)))
+  expect_equal(axes(imgarray), c("y", "x"))
+})
+
+test_that("replace axes of an ImageArray", {
+
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+
+  # axes can be permuted, all levels are permuted alike
+  axes(imgarray) <- c("y", "x", "c")
+  expect_equal(axes(imgarray), c("y", "x", "c"))
+  for(s in scales(imgarray))
+    expect_equal(names(s), c("y", "x", "c"))
+
+  # the scales follow their axes
+  expect_equal(scales(imgarray)[[2]], c(y = 0.4, x = 0.4, c = 1))
+
+  # the object remains valid
+  expect_true(validObject(imgarray))
+
+  # levels are untouched by the permutation
+  expect_equal(dim(imgarray[[1]]), c(3, 5, 5))
+})
+
+test_that("replace axes of an ImageArray with invalid axes", {
+
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+  msg <- "axes can only be replaced by a permutation of the existing axes"
+
+  # only permutations of the existing axes are allowed
+  expect_error(axes(imgarray) <- c("z", "y", "x"), msg)
+  expect_error(axes(imgarray) <- c("y", "x"), msg)
+  expect_error(axes(imgarray) <- c("c", "y", "x", "t"), msg)
+  expect_error(axes(imgarray) <- c("x", "x", "y"), msg)
+  expect_error(axes(imgarray) <- seq_len(3), msg)
+
+  # the object is left untouched
+  expect_equal(axes(imgarray), c("c", "y", "x"))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R
index a0e4c2d..7368904 100644
--- a/tests/testthat/test-scales.R
+++ b/tests/testthat/test-scales.R
@@ -42,4 +42,97 @@ test_that("get scales from number of levels", {
     .get_scales_from_nlevels(n.levels = 2, axes = c("c", "x")),
     "axes should have at least x and y dimensions!"
   )
+})
+
+test_that("get scales of an ImageArray", {
+
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+
+  # one named vector of scales per level
+  sc <- scales(imgarray)
+  expect_equal(length(sc), length(imgarray))
+  expect_equal(sc[[1]], c(c = 1, y = 1, x = 1))
+  expect_equal(sc[[2]], c(c = 1, y = 0.4, x = 0.4))
+})
+
+test_that("replace scales of an ImageArray", {
+
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+
+  # scales can be replaced with new values
+  scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
+                           c(c = 1, y = 0.5, x = 0.5))
+  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 0.5, x = 0.5))
+  expect_true(validObject(imgarray))
+
+  # the names of the scales may be a permutation of the existing axes,
+  # which in turn permutes the axes of the object
+  scales(imgarray) <- list(c(y = 1, x = 1, c = 1),
+                           c(y = 0.5, x = 0.5, c = 1))
+  expect_equal(axes(imgarray), c("y", "x", "c"))
+})
+
+test_that("replace scales of an ImageArray with invalid scales", {
+
+  imgarray <- ImageArray(image = list(array(1:75, dim = c(3,5,5)),
+                                      array(1:12, dim = c(3,2,2))),
+                         axes = c("c", "y", "x"))
+  msg <- paste0("names of each vector in scales should be a permutation of ",
+                "the existing axes")
+
+  # scales should be a list
+  expect_error(
+    scales(imgarray) <- c(c = 1, y = 1, x = 1),
+    "scales must be a list!"
+  )
+
+  # each vector should be named by a permutation of the existing axes
+  expect_error(scales(imgarray) <- list(c(1, 1, 1), c(1, 0.5, 0.5)), msg)
+  expect_error(
+    scales(imgarray) <- list(c(c = 1, y = 1, z = 1),
+                             c(c = 1, y = 0.5, z = 0.5)),
+    msg
+  )
+  expect_error(
+    scales(imgarray) <- list(c(y = 1, x = 1), c(y = 0.5, x = 0.5)),
+    msg
+  )
+  expect_error(
+    scales(imgarray) <- list(c(c = 1, y = 1, y = 1),
+                             c(c = 1, y = 0.5, y = 0.5)),
+    msg
+  )
+
+  # all levels should carry the same axes in the same order
+  expect_error(
+    scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
+                             c(y = 0.5, x = 0.5, c = 1)),
+    "scale names do not match axes"
+  )
+
+  # one vector of scales per level
+  expect_error(
+    scales(imgarray) <- list(c(c = 1, y = 1, x = 1)),
+    "scales should be of the same length as levels!"
+  )
+
+  # scales should be finite numbers
+  expect_error(
+    scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
+                             c(c = 1, y = Inf, x = 0.5)),
+    "scale entries are not numeric"
+  )
+  expect_error(
+    scales(imgarray) <- list(c(c = "1", y = "1", x = "1"),
+                             c(c = "1", y = "0.5", x = "0.5")),
+    "scale entries are not numeric"
+  )
+
+  # the object is left untouched
+  expect_equal(axes(imgarray), c("c", "y", "x"))
+  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 0.4, x = 0.4))
 })
\ No newline at end of file

From fd2d84c8d1db59d830be9b9487d64d2891e3eebf Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 22:50:30 +0200
Subject: [PATCH 5/9] update scaling strategy

---
 R/AllClasses.R                        |  2 --
 R/ImageArray.R                        | 15 ++++++++------
 R/manipulation.R                      |  4 ++--
 tests/testthat/test-array.R           |  4 ++--
 tests/testthat/test-axes.R            |  4 ++--
 tests/testthat/test-scales.R          | 28 +++++++++++++--------------
 tests/testthat/test-transformations.R |  2 +-
 7 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/R/AllClasses.R b/R/AllClasses.R
index 75b79bb..d7f80a7 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -6,8 +6,6 @@ NULL
 # magick classes
 setOldClass("magick-image")
 setOldClass("bitmap")
-setClassUnion(c("magick_class"), 
-              c("magick-image", "bitmap"))
 
 # array and matrix classes
 setClassUnion("matrix_array_Array", 
diff --git a/R/ImageArray.R b/R/ImageArray.R
index 5ac8e46..68c625e 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -403,8 +403,8 @@ createListFromEBImage <- function(
       if (verbose) .img_create_msg(dim_image, i)
       cur_image <- EBImage::resize(
         cur_image,
-        w = dim_image["x"]*scales[[i]]["x"],
-        h = dim_image["y"]*scales[[i]]["y"]
+        w = dim_image["x"]/scales[[i]]["x"],
+        h = dim_image["y"]/scales[[i]]["y"]
       )
       cur_img <- aperm(cur_image, perm = img_perm_backward)
       image_list[[i]] <-
@@ -446,7 +446,10 @@ createListFromList <- function(image,
 }
 
 #' @noRd
-setMethod("createImageList", "magick_class", createListFromMagick)
+setMethod("createImageList", "magick-image", createListFromMagick)
+
+#' @noRd
+setMethod("createImageList", "bitmap", createListFromMagick)
 
 #' @noRd
 setMethod("createImageList", "Image", createListFromEBImage)
@@ -865,7 +868,7 @@ setMethod("read_image",
 #' @keywords internal
 #' @noRd
 .magick_resize_scale <- function(dim_img, scales){
-  paste0(paste(round(dim_img*scales[c("x", "y")]), collapse = "x"),"!")
+  paste0(paste(round(dim_img/scales[c("x", "y")]), collapse = "x"),"!")
 }
 
 
@@ -882,7 +885,7 @@ setMethod("read_image",
     if(length(d) != length(axes)) stop(msg)
     d <- setNames(d, axes)
     sc <- .TEMPLATE_SCALES[axes]
-    sc[scaled_axes] <- d[scaled_axes]/first_dim[scaled_axes]
+    sc[scaled_axes] <- first_dim[scaled_axes]/d[scaled_axes]
     sc
   })
 }
@@ -894,7 +897,7 @@ setMethod("read_image",
     stop("axes should have at least x and y dimensions!")
   lapply(seq_len(n.levels), \(i){
     ax <- .TEMPLATE_SCALES[axes]
-    ax[c("x", "y")] <- ax[c("x", "y")] / 2^(i-1)
+    ax[c("x", "y")] <- ax[c("x", "y")] * 2^(i-1)
     ax
   })
 }
diff --git a/R/manipulation.R b/R/manipulation.R
index b452365..bc3f26a 100644
--- a/R/manipulation.R
+++ b/R/manipulation.R
@@ -74,8 +74,8 @@ setMethod("crop", signature = "ImageArray", function(object, index) {
       lapply(seq_along(index[scaled_axes]), function(j) {
         ind <- index[scaled_axes][[j]]
         ind <- c(
-          floor(ind[1] * cur_scale[scaled_axes][j]),
-          ceiling(ind[length(ind)] * cur_scale[scaled_axes][j])
+          floor(ind[1] / cur_scale[scaled_axes][j]),
+          ceiling(ind[length(ind)] / cur_scale[scaled_axes][j])
         )
         seq(max(ind[1], 1), min(ind[2], selected_dim[j]))
       })
diff --git a/tests/testthat/test-array.R b/tests/testthat/test-array.R
index 97fdb6a..7f48e38 100644
--- a/tests/testthat/test-array.R
+++ b/tests/testthat/test-array.R
@@ -70,7 +70,7 @@ test_that("array downscaled with EBImage and scales", {
   
   imgarray <- ImageArray(img3d, 
                          scales = list(c(x = 1, y = 1, c = 1),
-                                       c(x = 0.66, y = 0.2, c = 1)))
+                                       c(x = 1.5, y = 5, c = 1)))
   expect_equal(dim(imgarray[[2]]), c(13, 10, 3))
 })
 
@@ -78,7 +78,7 @@ test_that("array downscaled with magick and scales", {
   
   imgarray <- ImageArray(img3d, 
                          scales = list(c(x = 1, y = 1, c = 1),
-                                       c(x = 0.66, y = 0.2, c = 1)), 
+                                       c(x = 1.5, y = 5, c = 1)), 
                          engine = "magick-image")
   expect_equal(dim(imgarray[[2]]), c(13, 10, 3))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-axes.R b/tests/testthat/test-axes.R
index 92f4700..5930cff 100644
--- a/tests/testthat/test-axes.R
+++ b/tests/testthat/test-axes.R
@@ -76,7 +76,7 @@ test_that("duplicate axes", {
 test_that("get axes from scales", {
   
   scales <- list(c(x = 1, y = 1),
-                 c(x = 0.6, y = 0.6))
+                 c(x = 1.33, y = 1.33))
   axes <- .get_axes_from_scales(scales)
   expect_equal(axes, c("x", "y"))
   
@@ -123,7 +123,7 @@ test_that("replace axes of an ImageArray", {
     expect_equal(names(s), c("y", "x", "c"))
 
   # the scales follow their axes
-  expect_equal(scales(imgarray)[[2]], c(y = 0.4, x = 0.4, c = 1))
+  expect_equal(scales(imgarray)[[2]], c(y = 2.5, x = 2.5, c = 1))
 
   # the object remains valid
   expect_true(validObject(imgarray))
diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R
index 7368904..9354ea3 100644
--- a/tests/testthat/test-scales.R
+++ b/tests/testthat/test-scales.R
@@ -26,11 +26,11 @@ test_that("get scales from number of levels", {
   expect_equal(length(sc), 4)
   expect_equal(
     vapply(sc, \(.) .[["x"]], numeric(1)),
-    c(1, 0.5, 0.25, 0.125)
+    c(1, 2, 4, 8)
   )
   expect_equal(
     vapply(sc, \(.) .[["y"]], numeric(1)),
-    c(1, 0.5, 0.25, 0.125)
+    c(1, 2, 4, 8)
   )
   expect_equal(
     vapply(sc, \(.) .[["c"]], numeric(1)),
@@ -54,7 +54,7 @@ test_that("get scales of an ImageArray", {
   sc <- scales(imgarray)
   expect_equal(length(sc), length(imgarray))
   expect_equal(sc[[1]], c(c = 1, y = 1, x = 1))
-  expect_equal(sc[[2]], c(c = 1, y = 0.4, x = 0.4))
+  expect_equal(sc[[2]], c(c = 1, y = 2.5, x = 2.5))
 })
 
 test_that("replace scales of an ImageArray", {
@@ -65,14 +65,14 @@ test_that("replace scales of an ImageArray", {
 
   # scales can be replaced with new values
   scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
-                           c(c = 1, y = 0.5, x = 0.5))
-  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 0.5, x = 0.5))
+                           c(c = 1, y = 2, x = 2))
+  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 2, x = 2))
   expect_true(validObject(imgarray))
 
   # the names of the scales may be a permutation of the existing axes,
   # which in turn permutes the axes of the object
   scales(imgarray) <- list(c(y = 1, x = 1, c = 1),
-                           c(y = 0.5, x = 0.5, c = 1))
+                           c(y = 2, x = 2, c = 1))
   expect_equal(axes(imgarray), c("y", "x", "c"))
 })
 
@@ -91,26 +91,26 @@ test_that("replace scales of an ImageArray with invalid scales", {
   )
 
   # each vector should be named by a permutation of the existing axes
-  expect_error(scales(imgarray) <- list(c(1, 1, 1), c(1, 0.5, 0.5)), msg)
+  expect_error(scales(imgarray) <- list(c(1, 1, 1), c(1, 2, 2)), msg)
   expect_error(
     scales(imgarray) <- list(c(c = 1, y = 1, z = 1),
-                             c(c = 1, y = 0.5, z = 0.5)),
+                             c(c = 1, y = 2, z = 2)),
     msg
   )
   expect_error(
-    scales(imgarray) <- list(c(y = 1, x = 1), c(y = 0.5, x = 0.5)),
+    scales(imgarray) <- list(c(y = 1, x = 1), c(y = 2, x = 2)),
     msg
   )
   expect_error(
     scales(imgarray) <- list(c(c = 1, y = 1, y = 1),
-                             c(c = 1, y = 0.5, y = 0.5)),
+                             c(c = 1, y = 2, y = 2)),
     msg
   )
 
   # all levels should carry the same axes in the same order
   expect_error(
     scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
-                             c(y = 0.5, x = 0.5, c = 1)),
+                             c(y = 2, x = 2, c = 1)),
     "scale names do not match axes"
   )
 
@@ -123,16 +123,16 @@ test_that("replace scales of an ImageArray with invalid scales", {
   # scales should be finite numbers
   expect_error(
     scales(imgarray) <- list(c(c = 1, y = 1, x = 1),
-                             c(c = 1, y = Inf, x = 0.5)),
+                             c(c = 1, y = Inf, x = 2)),
     "scale entries are not numeric"
   )
   expect_error(
     scales(imgarray) <- list(c(c = "1", y = "1", x = "1"),
-                             c(c = "1", y = "0.5", x = "0.5")),
+                             c(c = "1", y = "2", x = "2")),
     "scale entries are not numeric"
   )
 
   # the object is left untouched
   expect_equal(axes(imgarray), c("c", "y", "x"))
-  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 0.4, x = 0.4))
+  expect_equal(scales(imgarray)[[2]], c(c = 1, y = 2.5, x = 2.5))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-transformations.R b/tests/testthat/test-transformations.R
index 8ba9e09..707933a 100644
--- a/tests/testthat/test-transformations.R
+++ b/tests/testthat/test-transformations.R
@@ -70,7 +70,7 @@ for(ni in names(img_list)) {
     od[xy] <- output.dim
     expect_equal(dim(imgarray_scale), od)
     for(i in seq_along(imgarray)){
-      od[xy] <- od[xy] / 2^(i-1)
+      od[xy] <- od[xy] * 2^(i-1)
       expect_equal(dim(imgarray_scale[[i]]), od)
     }
     

From b11c185ddaa694b6d71fa4a656b9e00aa54b8d76 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 23:03:36 +0200
Subject: [PATCH 6/9] fix transformation scaling

---
 R/transformations.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/transformations.R b/R/transformations.R
index 538a7e2..bc06e88 100644
--- a/R/transformations.R
+++ b/R/transformations.R
@@ -556,9 +556,9 @@ setMethod("affine",
             scl <- scales(x)
             for (i in seq_along(x@levels)) {
               sc <- scl[[i]][selected_axes]
-              m <- solve(diag(c(1/sc, 1))) %*% m %*% diag(1/sc) 
+              m <- solve(diag(c(sc, 1))) %*% m %*% diag(sc) 
               if(!is.null(output.dim)){
-                cur_output.dim <- output.dim * sc
+                cur_output.dim <- output.dim / sc
               } else {
                 cur_output.dim <- output.dim
               }
@@ -663,7 +663,7 @@ setMethod("scale",
             .check_outputdim(output.dim)
             for (i in seq_along(x@levels)) {
               sc <- scl[[i]][selected_axes]
-              cur_output.dim <- output.dim * sc
+              cur_output.dim <- output.dim / sc
               x[[i]] <- .scale_transform(
                 x[[i]],
                 output.dim = cur_output.dim,

From 92d9b165c04adc9f128896872f6b9a6c64512ae0 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 23:05:27 +0200
Subject: [PATCH 7/9] some fixes

---
 R/Validity.R                 | 1 -
 tests/testthat/test-array.R  | 2 +-
 tests/testthat/test-axes.R   | 2 +-
 tests/testthat/test-scales.R | 2 +-
 4 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/R/Validity.R b/R/Validity.R
index e252c4a..18d224f 100644
--- a/R/Validity.R
+++ b/R/Validity.R
@@ -3,7 +3,6 @@
   # check scales vs levels, this is done first since the axes are
   # given by the names of the scales
   sc <- scales(object)
-  if (!is.list(sc)) stop("scales must be a list!")
   if(length(sc) != length(object@levels))
     stop("scales should be of the same length as levels!")
 
diff --git a/tests/testthat/test-array.R b/tests/testthat/test-array.R
index 7f48e38..344e032 100644
--- a/tests/testthat/test-array.R
+++ b/tests/testthat/test-array.R
@@ -81,4 +81,4 @@ test_that("array downscaled with magick and scales", {
                                        c(x = 1.5, y = 5, c = 1)), 
                          engine = "magick-image")
   expect_equal(dim(imgarray[[2]]), c(13, 10, 3))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-axes.R b/tests/testthat/test-axes.R
index 5930cff..c45376d 100644
--- a/tests/testthat/test-axes.R
+++ b/tests/testthat/test-axes.R
@@ -148,4 +148,4 @@ test_that("replace axes of an ImageArray with invalid axes", {
 
   # the object is left untouched
   expect_equal(axes(imgarray), c("c", "y", "x"))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-scales.R b/tests/testthat/test-scales.R
index 9354ea3..c94459d 100644
--- a/tests/testthat/test-scales.R
+++ b/tests/testthat/test-scales.R
@@ -135,4 +135,4 @@ test_that("replace scales of an ImageArray with invalid scales", {
   # the object is left untouched
   expect_equal(axes(imgarray), c("c", "y", "x"))
   expect_equal(scales(imgarray)[[2]], c(c = 1, y = 2.5, x = 2.5))
-})
\ No newline at end of file
+})

From 6267452d3e71d4dcafc4bbff36c987011364edda Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Sat, 8 Aug 2026 23:33:15 +0200
Subject: [PATCH 8/9] make replace methods internal

---
 NAMESPACE               | 2 --
 R/AllClasses.R          | 1 -
 R/ImageArray.R          | 2 --
 man/ImageArray-class.Rd | 1 -
 4 files changed, 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index a983ad0..7211294 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,7 +11,6 @@ exportClasses(ImageArray)
 exportMethods("[")
 exportMethods("[[")
 exportMethods("[[<-")
-exportMethods("axes<-")
 exportMethods("path<-")
 exportMethods("scales<-")
 exportMethods(affine)
@@ -31,7 +30,6 @@ exportMethods(realize)
 exportMethods(resolution)
 exportMethods(rotate)
 exportMethods(scale)
-exportMethods(scales)
 exportMethods(series)
 exportMethods(translation)
 exportMethods(type)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index d7f80a7..f29df09 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -31,7 +31,6 @@ setClassUnion("matrix_array_Array",
 #'   and are shared, in the same order, by all levels. See
 #'   \url{https://ngff.openmicroscopy.org/} for more information.
 #'
-#' @keywords internal
 #' @exportClass ImageArray
 .ImageArray <- setClass(
   Class = "ImageArray",
diff --git a/R/ImageArray.R b/R/ImageArray.R
index 68c625e..af1317d 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -192,7 +192,6 @@ setMethod("axes", "ImageArray", function(object)
 
 #' @describeIn ImageArray-methods replace axes metadata of the ImageArray
 #' object, the replacement can only be a permutation of the existing axes
-#' @exportMethod axes<-
 setReplaceMethod("axes", "ImageArray", function(object, ..., value){
   ax <- axes(object)
   
@@ -208,7 +207,6 @@ setReplaceMethod("axes", "ImageArray", function(object, ..., value){
 })
 
 #' @describeIn ImageArray-methods get scales metadata of the ImageArray object
-#' @exportMethod scales
 setMethod("scales", "ImageArray", function(object) object@scales)
 
 #' @describeIn ImageArray-methods replace scales metadata of the ImageArray
diff --git a/man/ImageArray-class.Rd b/man/ImageArray-class.Rd
index fb73890..c1b4e26 100644
--- a/man/ImageArray-class.Rd
+++ b/man/ImageArray-class.Rd
@@ -23,4 +23,3 @@ and are shared, in the same order, by all levels. See
 \url{https://ngff.openmicroscopy.org/} for more information.}
 }}
 
-\keyword{internal}

From 0457eeaf6649e59ebd49a5ea0de4804c3baa3516 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Mon, 10 Aug 2026 14:19:50 +0200
Subject: [PATCH 9/9] fix some issues, update NEWS

---
 NEWS.md                               | 11 +++++++++++
 tests/testthat/test-transformations.R |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index a623592..5fec2e7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,14 @@
+# ImageArray 1.1.7
+
+## New features
+
+* Compatibility with https://github.com/Huber-group-EMBL/romeo
+* `ImageArray` class is now exported.
+* `axes` slot is dropped from `ImageArray` class and now parsed from 
+  names(scales(object)[[1]]) (which can still be parsed from `axes(object)` 
+  as usual).
+* scales of pyramid axes are now inverted, e.g. 1, 0.5, 0.125 are now 1, 2, 4. 
+  
 # ImageArray 1.1.6
 
 ## New features
diff --git a/tests/testthat/test-transformations.R b/tests/testthat/test-transformations.R
index 707933a..8ba9e09 100644
--- a/tests/testthat/test-transformations.R
+++ b/tests/testthat/test-transformations.R
@@ -70,7 +70,7 @@ for(ni in names(img_list)) {
     od[xy] <- output.dim
     expect_equal(dim(imgarray_scale), od)
     for(i in seq_along(imgarray)){
-      od[xy] <- od[xy] * 2^(i-1)
+      od[xy] <- od[xy] / 2^(i-1)
       expect_equal(dim(imgarray_scale[[i]]), od)
     }