From 43039b2cb76c86fe6afb9974b26cff849fe81633 Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Thu, 28 May 2026 17:16:54 +0200
Subject: [PATCH 1/9] support >2/3D

---
 NAMESPACE          |  1 -
 R/sdArray.R        |  4 ++--
 R/sdAttrs.R        |  5 ++++-
 R/validity.R       | 10 ++++++----
 man/SpatialData.Rd |  6 ++++--
 5 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 1643cccc..fdfe35ef 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -130,7 +130,6 @@ importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
-importFrom(S4Vectors,isSequence)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)
diff --git a/R/sdArray.R b/R/sdArray.R
index bc4ac5c6..dde5a940 100644
--- a/R/sdArray.R
+++ b/R/sdArray.R
@@ -133,12 +133,12 @@ setMethod("channels", "SpatialDataImage", \(x, ...) channels(meta(x)))
 setMethod("channels", "SpatialDataElement", \(x, ...) stop("only 'images' have channels"))
 
 # compares metadata dataset paths to arrays on disk
-#' @importFrom S4Vectors isSequence
 .validate_multiscales_paths <- function(x, ds) {
     ps <- list.files(x)
     ds <- ds[ds %in% ps]
     if (!length(ds))
-      stop("Invalid SpatialData image or label: metadata does not match the names of Zarr arrays")
+        stop("Invalid 'SpatialData' image or label:",
+            " metadata does not match the names of Zarr arrays")
     return(ds)
 }
 
diff --git a/R/sdAttrs.R b/R/sdAttrs.R
index 8d03ae1b..16801f1b 100644
--- a/R/sdAttrs.R
+++ b/R/sdAttrs.R
@@ -127,7 +127,10 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 # internal use only!
 #' @noRd 
 .zv <- \(x) {
-    v <- x$spatialdata_attrs$version
+    v <- x$ome$version %||%
+        x$omero$version %||%
+        x$multiscales[[1]]$version %||%
+        x$spatialdata_attrs$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
     ok <- length(v) == 1 && is.character(v) && v %in% sprintf("0.%d", seq_len(5))
     if (!ok) stop("invalid 'version' in 'spatialdata_attrs'; expected '0.x' where x is 1-5")
diff --git a/R/validity.R b/R/validity.R
index 7906e3d6..c757c52c 100644
--- a/R/validity.R
+++ b/R/validity.R
@@ -49,10 +49,11 @@
 .validateImage <- \(object) {
     msg <- c()
     res <- length(object)
+    d <- length(dim(object))
     for (k in seq_len(res)) {
         x <- data(object, k)
-        if (length(dim(x)) != 3) msg <- c(msg, paste(
-            "'SpatialDataImage' resolution", k, "is not 3D"))
+        if (length(dim(x)) != d) msg <- c(msg, paste(
+            "'SpatialDataImage' resolution", k, "is not ", d, "D"))
         if (!type(x) %in% c("double", "integer")) msg <- c(msg, paste(
             "'SpatialDataImage' resolution", k, "is not of type double or integer"))
     }
@@ -65,10 +66,11 @@ setValidity2("SpatialDataImage", .validateImage)
 .validateLabel <- \(object) {
     msg <- c()
     res <- length(object)
+    d <- length(axes(object))
     for (k in seq_len(res)) {
         x <- data(object, k)
-        if (length(dim(x)) != 2) msg <- c(msg, paste(
-            "'SpatialDataLabel' resolution", k, "is not 2D"))
+        if (length(dim(x)) != d) msg <- c(msg, paste(
+            "'SpatialDataLabel' resolution", k, "is not ", d, "D"))
         if (type(x) != "integer") msg <- c(msg, paste(
             "'SpatialDataLabel' resolution", k, "is not of type integer"))
     }
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index 7390113d..f377ade8 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -63,6 +63,8 @@
 \alias{points,SpatialData-method}
 \alias{shapes,SpatialData-method}
 \alias{tables,SpatialData-method}
+\alias{[[<-,SpatialData,numeric,ANY,ANY-method}
+\alias{[[<-,SpatialData,character,ANY,ANY-method}
 \title{The `SpatialData` class}
 \usage{
 SpatialData(images, labels, points, shapes, tables)
@@ -109,9 +111,9 @@ SpatialData(images, labels, points, shapes, tables)
 
 \S4method{tables}{SpatialData}(x)
 
-\S4method{[[}{SpatialData,numeric,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,numeric,ANY,ANY}(x, i) <- value
 
-\S4method{[[}{SpatialData,character,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,character,ANY,ANY}(x, i) <- value
 }
 \arguments{
 \item{images}{list of \code{\link{SpatialDataImage}}s}

From 71514b26f168f6842d3dbbae42fb88b86ea5df6e Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 09:01:09 +0200
Subject: [PATCH 2/9] fix tests; use new BiocGenerics

---
 NAMESPACE                     |  4 +++-
 R/AllGenerics.R               |  6 +++---
 R/sdAttrs.R                   |  9 +++++----
 R/trans.R                     | 21 +++++++++++----------
 R/validity.R                  |  8 ++++++--
 man/SpatialData.Rd            |  6 ++----
 man/trans.Rd                  | 20 ++++++++++----------
 tests/testthat/test-sdattrs.R |  4 +---
 8 files changed, 41 insertions(+), 37 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 4c0c716f..2b7e109e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -115,12 +115,14 @@ exportMethods(translation)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
+importFrom(BiocGenerics,rotate)
 importFrom(BiocGenerics,rownames)
+importFrom(BiocGenerics,scale)
+importFrom(BiocGenerics,sequence)
 importFrom(BiocGenerics,table)
 importFrom(BiocGenerics,transform)
 importFrom(DBI,dbIsValid)
 importFrom(DelayedArray,DelayedArray)
-importFrom(EBImage,rotate)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,sparseVector)
 importFrom(Matrix,summary)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 1ab28674..88b269c6 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -57,9 +57,9 @@ setGeneric("CTgraph", \(x, ...) standardGeneric("CTgraph"))
 setGeneric("rmvCT", \(x, ...) standardGeneric("rmvCT"))
 setGeneric("addCT", \(x, ...) standardGeneric("addCT"))
 
-setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
-setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
-setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
+#setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
+#setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
+#setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
 setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
 setGeneric("flip", \(x, ...) standardGeneric("flip"))
diff --git a/R/sdAttrs.R b/R/sdAttrs.R
index 16801f1b..018d5916 100644
--- a/R/sdAttrs.R
+++ b/R/sdAttrs.R
@@ -127,12 +127,13 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 # internal use only!
 #' @noRd 
 .zv <- \(x) {
-    v <- x$ome$version %||%
-        x$omero$version %||%
+    v <- 
+        x$spatialdata_attrs$version %||%
         x$multiscales[[1]]$version %||%
-        x$spatialdata_attrs$version
+        x$omero$version %||%
+        x$ome$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
-    ok <- length(v) == 1 && is.character(v) && v %in% sprintf("0.%d", seq_len(5))
+    ok <- length(v) == 1 && is.character(v) && gsub("-.*", "", v) %in% sprintf("0.%d", seq_len(5))
     if (!ok) stop("invalid 'version' in 'spatialdata_attrs'; expected '0.x' where x is 1-5")
     return(v)
 }
diff --git a/R/trans.R b/R/trans.R
index 2af78569..94f806fd 100644
--- a/R/trans.R
+++ b/R/trans.R
@@ -48,9 +48,9 @@
 #' y["shapes", c("rot", "wide", "left")]
 NULL
 
-#' @importFrom BiocGenerics transform
 #' @export
 #' @rdname trans
+#' @importFrom BiocGenerics transform
 setMethod("transform", "SpatialDataElement", \(x, i=1, ...) {
     stopifnot(
         length(i) == 1, is.character(i) | 
@@ -70,7 +70,8 @@ setMethod("transform", "SpatialDataElement", \(x, i=1, ...) {
 
 #' @export
 #' @rdname trans
-setMethod("sequence", c("SpatialDataElement", "list"), \(x, t, ..., rev=FALSE) {
+#' @importFrom BiocGenerics sequence
+setMethod("sequence", "SpatialDataElement", \(x, t, ..., rev=FALSE) {
     if (rev) t <- rev(t)
     for (. in seq_along(t)) {
         if (is.null(t[[.]])) next
@@ -108,9 +109,9 @@ setMethod("flop", "SpatialDataArray", \(x, k=1, ...) .mirror(x, 90, k))
 #' @export
 #' @rdname trans
 #' @importFrom methods as
-#' @importFrom EBImage rotate
+#' @importFrom BiocGenerics rotate
 #' @importFrom S4Vectors metadata<-
-setMethod("rotate", c("SpatialDataArray", "numeric"), \(x, t, k=1, ..., rev=FALSE) {
+setMethod("rotate", "SpatialDataArray", \(x, t, k=1, ..., rev=FALSE) {
     # negate angle since 'EBImage' rotates clockwise
     stopifnot(length(t) == 1, is.finite(t))
     if (t %% 360 == 0) return(x)
@@ -151,8 +152,8 @@ setMethod("rotate", c("SpatialDataArray", "numeric"), \(x, t, k=1, ..., rev=FALS
 
 #' @export
 #' @rdname trans
-setMethod("scale", 
-    c("SpatialDataArray", "numeric"), 
+#' @importFrom BiocGenerics scale
+setMethod("scale", "SpatialDataArray",
     \(x, t, ...) .trans_a(x, t, "scale", ...))
 
 #' @export
@@ -204,14 +205,14 @@ setMethod("translation",
 
 #' @export
 #' @rdname trans
-setMethod("rotate", 
-    c("SpatialDataFrame", "numeric"), 
+#' @importFrom BiocGenerics rotate
+setMethod("rotate", "SpatialDataFrame",
     \(x, t, ...) .trans_f(x, t, "rotate", ...))
 
 #' @export
 #' @rdname trans
-setMethod("scale", 
-    c("SpatialDataFrame", "numeric"), 
+#' @importFrom BiocGenerics scale
+setMethod("scale", "SpatialDataFrame",
     \(x, t, ...) .trans_f(x, t, "scale", ...))
 
 #' @export
diff --git a/R/validity.R b/R/validity.R
index c757c52c..d609fc92 100644
--- a/R/validity.R
+++ b/R/validity.R
@@ -49,7 +49,9 @@
 .validateImage <- \(object) {
     msg <- c()
     res <- length(object)
-    d <- length(dim(object))
+    axs <- axes(object)
+    typ <- vapply(axs, \(.) .$type, character(1))
+    d <- sum(typ != "time")
     for (k in seq_len(res)) {
         x <- data(object, k)
         if (length(dim(x)) != d) msg <- c(msg, paste(
@@ -66,7 +68,9 @@ setValidity2("SpatialDataImage", .validateImage)
 .validateLabel <- \(object) {
     msg <- c()
     res <- length(object)
-    d <- length(axes(object))
+    axs <- axes(object)
+    typ <- vapply(axs, \(.) .$type, character(1))
+    d <- sum(typ == "space")
     for (k in seq_len(res)) {
         x <- data(object, k)
         if (length(dim(x)) != d) msg <- c(msg, paste(
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index f377ade8..7390113d 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -63,8 +63,6 @@
 \alias{points,SpatialData-method}
 \alias{shapes,SpatialData-method}
 \alias{tables,SpatialData-method}
-\alias{[[<-,SpatialData,numeric,ANY,ANY-method}
-\alias{[[<-,SpatialData,character,ANY,ANY-method}
 \title{The `SpatialData` class}
 \usage{
 SpatialData(images, labels, points, shapes, tables)
@@ -111,9 +109,9 @@ SpatialData(images, labels, points, shapes, tables)
 
 \S4method{tables}{SpatialData}(x)
 
-\S4method{[[}{SpatialData,numeric,ANY,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,numeric,ANY}(x, i) <- value
 
-\S4method{[[}{SpatialData,character,ANY,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,character,ANY}(x, i) <- value
 }
 \arguments{
 \item{images}{list of \code{\link{SpatialDataImage}}s}
diff --git a/man/trans.Rd b/man/trans.Rd
index 447ec9a2..1555c6ec 100644
--- a/man/trans.Rd
+++ b/man/trans.Rd
@@ -11,21 +11,21 @@
 \alias{mirror}
 \alias{sequence}
 \alias{transform,SpatialDataElement-method}
-\alias{sequence,SpatialDataElement,list-method}
+\alias{sequence,SpatialDataElement-method}
 \alias{mirror,SpatialDataArray-method}
 \alias{flip,SpatialDataArray-method}
 \alias{flop,SpatialDataArray-method}
-\alias{rotate,SpatialDataArray,numeric-method}
-\alias{scale,SpatialDataArray,numeric-method}
+\alias{rotate,SpatialDataArray-method}
+\alias{scale,SpatialDataArray-method}
 \alias{translation,SpatialDataArray,numeric-method}
-\alias{rotate,SpatialDataFrame,numeric-method}
-\alias{scale,SpatialDataFrame,numeric-method}
+\alias{rotate,SpatialDataFrame-method}
+\alias{scale,SpatialDataFrame-method}
 \alias{translation,SpatialDataFrame,numeric-method}
 \title{Transformations}
 \usage{
 \S4method{transform}{SpatialDataElement}(x, i = 1, ...)
 
-\S4method{sequence}{SpatialDataElement,list}(x, t, ..., rev = FALSE)
+\S4method{sequence}{SpatialDataElement}(x, t, ..., rev = FALSE)
 
 \S4method{mirror}{SpatialDataArray}(x, t = c("v", "h"), k = 1, ...)
 
@@ -33,15 +33,15 @@
 
 \S4method{flop}{SpatialDataArray}(x, k = 1, ...)
 
-\S4method{rotate}{SpatialDataArray,numeric}(x, t, k = 1, ..., rev = FALSE)
+\S4method{rotate}{SpatialDataArray}(x, t, k = 1, ..., rev = FALSE)
 
-\S4method{scale}{SpatialDataArray,numeric}(x, t, ...)
+\S4method{scale}{SpatialDataArray}(x, t, ...)
 
 \S4method{translation}{SpatialDataArray,numeric}(x, t, ...)
 
-\S4method{rotate}{SpatialDataFrame,numeric}(x, t, ...)
+\S4method{rotate}{SpatialDataFrame}(x, t, ...)
 
-\S4method{scale}{SpatialDataFrame,numeric}(x, t, ...)
+\S4method{scale}{SpatialDataFrame}(x, t, ...)
 
 \S4method{translation}{SpatialDataFrame,numeric}(x, t, ...)
 }
diff --git a/tests/testthat/test-sdattrs.R b/tests/testthat/test-sdattrs.R
index 0424164a..63cc1fca 100644
--- a/tests/testthat/test-sdattrs.R
+++ b/tests/testthat/test-sdattrs.R
@@ -11,8 +11,6 @@ for (v in names(z)) {
         z <- multiscales(y)
         expect_is(z, "list")
         expect_length(z, 1)
-        y$spatialdata_attrs <- NULL
-        expect_error(multiscales(y))
     })
 
     test_that(paste0(v, "-axes"), {
@@ -48,4 +46,4 @@ for (v in names(z)) {
         expect_length(z, dim(y)[1])
     })
 
-}
\ No newline at end of file
+}

From 02106e89a284521cca7fd9bc0a21e29af8557081 Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 09:27:27 +0200
Subject: [PATCH 3/9] revise ome(ro) version retrieval

---
 R/CTutils.R |  3 ++-
 R/sdArray.R |  2 +-
 R/sdAttrs.R | 11 +++++++----
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/CTutils.R b/R/CTutils.R
index 09c09dc3..5f281096 100644
--- a/R/CTutils.R
+++ b/R/CTutils.R
@@ -219,7 +219,8 @@ setMethod("addCT", "SpatialDataAttrs", \(x, name, type="identity", data=NULL) {
     if (is.null(multiscales(x))) {
         x[[ct]] <- new
     } else {
-        switch(.zv(x), 
+        switch( 
+            tryCatch(.zv(x), error=\(e) "9.9"), 
             "0.3"=x$ome[[ms]][[1]][[ct]] <- new,
             x[[ms]][[1]][[ct]] <- new)
     }
diff --git a/R/sdArray.R b/R/sdArray.R
index dde5a940..3b21c056 100644
--- a/R/sdArray.R
+++ b/R/sdArray.R
@@ -116,7 +116,7 @@ setMethod("data_type", "DelayedArray", \(x) {
 # internal use only!
 #' @noRd 
 .ch <- \(x) {
-    if (.zv(x) == "0.3") x <- x$ome
+    if (.zv(x) == "0.5") x <- x$ome
     unlist(x$omero$channels)
 }
 
diff --git a/R/sdAttrs.R b/R/sdAttrs.R
index 018d5916..5e52a750 100644
--- a/R/sdAttrs.R
+++ b/R/sdAttrs.R
@@ -128,19 +128,22 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 #' @noRd 
 .zv <- \(x) {
     v <- 
-        x$spatialdata_attrs$version %||%
         x$multiscales[[1]]$version %||%
-        x$omero$version %||%
+        x$omero$version %||% 
         x$ome$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
-    ok <- length(v) == 1 && is.character(v) && gsub("-.*", "", v) %in% sprintf("0.%d", seq_len(5))
+    ok <- length(v) == 1 && is.character(v) && (v <- gsub("-.*", "", v)) %in% sprintf("0.%d", seq_len(5))
     if (!ok) stop("invalid 'version' in 'spatialdata_attrs'; expected '0.x' where x is 1-5")
     return(v)
 }
 
 # internal use only!
 #' @noRd 
-.ms <- \(x) switch(.zv(x), "0.3"=x$ome$multiscales, x$multiscales)
+.ms <- \(x) {
+    v <- tryCatch(.zv(x), error=\(e) NULL)
+    if (is.null(v)) return()
+    switch(v, "0.5"=x$ome$multiscales, x$multiscales)
+}
 
 # internal use only!
 #' @noRd 

From e2acbbd39e142067f32d3c2e24dc73d0216b82ba Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 10:49:00 +0200
Subject: [PATCH 4/9] remove praws, move EBImage to Suggests:

---
 DESCRIPTION | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9d87adbd..eab83ee8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -58,7 +58,6 @@ Imports:
     DelayedArray,
     dplyr,
     duckspatial,
-    EBImage,
     graph,
     Matrix,
     methods,
@@ -73,8 +72,8 @@ Imports:
     ZarrArray
 Suggests:
     BiocStyle,
+    EBImage,
     knitr,
-    paws,
     Rgraphviz,
     testthat
 biocViews: 

From faa0884974920a320b152e482afae1417f875c5d Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 10:49:12 +0200
Subject: [PATCH 5/9] fix version retrieval for frames

---
 R/sdArray.R | 4 +++-
 R/trans.R   | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/sdArray.R b/R/sdArray.R
index 3b21c056..5fd42c64 100644
--- a/R/sdArray.R
+++ b/R/sdArray.R
@@ -116,7 +116,9 @@ setMethod("data_type", "DelayedArray", \(x) {
 # internal use only!
 #' @noRd 
 .ch <- \(x) {
-    if (.zv(x) == "0.5") x <- x$ome
+    v <- tryCatch(.zv(x), error=\(e) NULL)
+    if (is.null(v)) return()
+    if (v == "0.5") x <- x$ome
     unlist(x$omero$channels)
 }
 
diff --git a/R/trans.R b/R/trans.R
index 94f806fd..e4109511 100644
--- a/R/trans.R
+++ b/R/trans.R
@@ -112,6 +112,8 @@ setMethod("flop", "SpatialDataArray", \(x, k=1, ...) .mirror(x, 90, k))
 #' @importFrom BiocGenerics rotate
 #' @importFrom S4Vectors metadata<-
 setMethod("rotate", "SpatialDataArray", \(x, t, k=1, ..., rev=FALSE) {
+    if (!requireNamespace("EBImage", quietly=TRUE))
+        stop("install 'EBImage' to use this function")
     # negate angle since 'EBImage' rotates clockwise
     stopifnot(length(t) == 1, is.finite(t))
     if (t %% 360 == 0) return(x)

From 67f1b14872940e064553d19c2e24a6472d3352ee Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 11:06:43 +0200
Subject: [PATCH 6/9] fix combine test

---
 tests/testthat/test-combine.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-combine.R b/tests/testthat/test-combine.R
index 72f7af00..b52fe302 100644
--- a/tests/testthat/test-combine.R
+++ b/tests/testthat/test-combine.R
@@ -4,7 +4,6 @@ x <- readSpatialData(x)
 
 test_that("combine", {
     # auto-fixed names
-    expect_error(combine(x))
     expect_no_message(y <- combine(x, x))
     f <- \(.) unlist(colnames(.))
     expect_all_true(f(x) %in% f(y))

From 1fc8a5658a3da86e499e01893824296ac5b140e3 Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Fri, 29 May 2026 15:58:32 +0200
Subject: [PATCH 7/9] address HG comments

---
 R/AllGenerics.R | 6 +-----
 R/CTutils.R     | 2 +-
 R/sdArray.R     | 2 +-
 R/sdAttrs.R     | 8 ++++----
 4 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 88b269c6..2e3bea24 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -57,14 +57,10 @@ setGeneric("CTgraph", \(x, ...) standardGeneric("CTgraph"))
 setGeneric("rmvCT", \(x, ...) standardGeneric("rmvCT"))
 setGeneric("addCT", \(x, ...) standardGeneric("addCT"))
 
-#setGeneric("scale", \(x, t, ...) standardGeneric("scale"))
-#setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
-#setGeneric("sequence", \(x, t, ...) standardGeneric("sequence"))
-setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
-
 setGeneric("flip", \(x, ...) standardGeneric("flip"))
 setGeneric("flop", \(x, ...) standardGeneric("flop"))
 setGeneric("mirror", \(x, ...) standardGeneric("mirror"))
+setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
 # sda ----
 
diff --git a/R/CTutils.R b/R/CTutils.R
index 5f281096..5c471d58 100644
--- a/R/CTutils.R
+++ b/R/CTutils.R
@@ -220,7 +220,7 @@ setMethod("addCT", "SpatialDataAttrs", \(x, name, type="identity", data=NULL) {
         x[[ct]] <- new
     } else {
         switch( 
-            tryCatch(.zv(x), error=\(e) "9.9"), 
+            tryCatch(.ome_ver(x), error=\(e) "9.9"), 
             "0.3"=x$ome[[ms]][[1]][[ct]] <- new,
             x[[ms]][[1]][[ct]] <- new)
     }
diff --git a/R/sdArray.R b/R/sdArray.R
index 5fd42c64..12aaf696 100644
--- a/R/sdArray.R
+++ b/R/sdArray.R
@@ -116,7 +116,7 @@ setMethod("data_type", "DelayedArray", \(x) {
 # internal use only!
 #' @noRd 
 .ch <- \(x) {
-    v <- tryCatch(.zv(x), error=\(e) NULL)
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
     if (is.null(v)) return()
     if (v == "0.5") x <- x$ome
     unlist(x$omero$channels)
diff --git a/R/sdAttrs.R b/R/sdAttrs.R
index 5e52a750..7f6ae526 100644
--- a/R/sdAttrs.R
+++ b/R/sdAttrs.R
@@ -126,21 +126,21 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 
 # internal use only!
 #' @noRd 
-.zv <- \(x) {
+.ome_ver <- \(x) {
     v <- 
         x$multiscales[[1]]$version %||%
         x$omero$version %||% 
         x$ome$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
-    ok <- length(v) == 1 && is.character(v) && (v <- gsub("-.*", "", v)) %in% sprintf("0.%d", seq_len(5))
-    if (!ok) stop("invalid 'version' in 'spatialdata_attrs'; expected '0.x' where x is 1-5")
+    ok <- length(v) == 1 && is.character(v) && (v <- gsub("-.*", "", v)) %in% sprintf("0.%d", seq_len(6))
+    if (!ok) stop("invalid OME 'version'; expected '0.x' where x is 1-5")
     return(v)
 }
 
 # internal use only!
 #' @noRd 
 .ms <- \(x) {
-    v <- tryCatch(.zv(x), error=\(e) NULL)
+    v <- tryCatch(.ome_ver(x), error=\(e) NULL)
     if (is.null(v)) return()
     switch(v, "0.5"=x$ome$multiscales, x$multiscales)
 }

From d97d035b9dfa3ee31bc27d549d684eb8af93c214 Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Sat, 30 May 2026 10:41:12 +0200
Subject: [PATCH 8/9] use BiocGenerics::data

---
 NAMESPACE          |  1 +
 R/AllGenerics.R    |  4 +---
 R/methods.R        | 11 +++--------
 man/SpatialData.Rd |  4 ++--
 4 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 6563c390..33a80a63 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -115,6 +115,7 @@ exportMethods(translation)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)
+importFrom(BiocGenerics,data)
 importFrom(BiocGenerics,rownames)
 importFrom(BiocGenerics,table)
 importFrom(BiocGenerics,transform)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 1ab28674..ad04d4d5 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -83,11 +83,9 @@ setGeneric("instance_key<-", \(x, value) standardGeneric("instance_key<-"))
 
 # uts ----
 
-setGeneric("data", \(...) standardGeneric("data"))
 setGeneric("meta", \(x, ...) standardGeneric("meta"))
-
-setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 setGeneric("meta<-", \(x, ..., value) standardGeneric("meta<-"))
+setGeneric("data<-", \(x, ..., value) standardGeneric("data<-"))
 
 setGeneric("layer", \(x, i, ...) standardGeneric("layer"))
 setGeneric("element", \(x, i, ...) standardGeneric("element"))
diff --git a/R/methods.R b/R/methods.R
index 6e26ef21..1f341393 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -27,15 +27,10 @@ setMethod("[[", c("SpatialData", "character"), \(x, i, ...) attr(x, i))
 
 #' @export
 #' @rdname SpatialData
-setMethod("data", "ANY", \(...) {
-    l <- list(...)
-    x <- l[[1]]
-    if (!is(x, "SpatialDataElement")) 
-        return(utils::data(...))
-    if (!is(x, "SpatialDataArray")) 
-        return(x@data)
+#' @importFrom BiocGenerics data
+setMethod("data", "SpatialDataElement", \(x, k=1, ...) {
+    if (!is(x, "SpatialDataArray")) return(x@data)
     # return list of available scales
-    k <- if (length(l) == 1) 1 else l[[2]]
     if (is.null(k)) return(x@data)
     # should be a scalar positive integer
     ok <- length(k) == 1 && is.numeric(k) && k > 0 && k == round(k)
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index 7390113d..bcf65623 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -46,7 +46,7 @@
 \alias{$<-,SpatialData-method}
 \alias{[[,SpatialData,numeric,ANY-method}
 \alias{[[,SpatialData,character,ANY-method}
-\alias{data,ANY-method}
+\alias{data,SpatialDataElement-method}
 \alias{meta,SpatialDataElement-method}
 \alias{[,SpatialData,ANY,ANY,ANY-method}
 \alias{rownames,SpatialData-method}
@@ -75,7 +75,7 @@ SpatialData(images, labels, points, shapes, tables)
 
 \S4method{[[}{SpatialData,character,ANY}(x, i, j, ...)
 
-\S4method{data}{ANY}(...)
+\S4method{data}{SpatialDataElement}(x, k = 1, ...)
 
 \S4method{meta}{SpatialDataElement}(x)
 

From 31a66cac2296063f1a816d3fde5576cd490f17c9 Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Sat, 30 May 2026 11:01:37 +0200
Subject: [PATCH 9/9] fix typo

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

diff --git a/DESCRIPTION b/DESCRIPTION
index c7104712..dc81ffe6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,7 @@ Authors@R: c(
     person("Vince", "Carey",
         role=c("aut"),
         email="stvjc@channing.harvard.edu",
-        comment=c(ORCID="0000-0003-4046-0063"))
+        comment=c(ORCID="0000-0003-4046-0063")))
 Imports:
     anndataR (>= 1.1.3),
     BiocGenerics,