diff --git a/.gitignore b/.gitignore
index 7ac4af56..a110dd34 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ inst/extdata/xenium1.zarr
 inst/extdata/visiumhd.zarr
 *.Rproj
 *.html
+R/_*
diff --git a/DESCRIPTION b/DESCRIPTION
index 8fbcafc8..7438d1bc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.6)
-Version: 0.99.28
+Version: 0.99.29
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufacturer
     data and writing to .zarr, on-disk representation of images/labels as
@@ -51,7 +51,6 @@ Imports:
     sf,
     S4Arrays,
     S4Vectors,
-    SparseArray,
     SingleCellExperiment,
     SummarizedExperiment
 Suggests:
@@ -63,8 +62,7 @@ Suggests:
     Rgraphviz,
     SpatialData.data,
     SpatialData.plot,
-    testthat,
-    DT
+    testthat
 Remotes:
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index cc2107a1..62ae3d87 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -40,7 +40,6 @@ setGeneric("tables<-", \(x, value) standardGeneric("tables<-"))
 
 # trs ----
 
-setGeneric("axes", \(x, ...) standardGeneric("axes"))
 setGeneric("CTlist", \(x, ...) standardGeneric("CTlist"))
 setGeneric("CTdata", \(x, ...) standardGeneric("CTdata"))
 setGeneric("CTname", \(x, ...) standardGeneric("CTname"))
@@ -79,11 +78,13 @@ setGeneric("meta", \(x, ...) standardGeneric("meta"))
 setGeneric("query", \(x, ...) standardGeneric("query"))
 setGeneric("mask", \(x, i, j, ...) standardGeneric("mask"))
 
+setGeneric("axes", \(x, ...) standardGeneric("axes"))
+setGeneric("extent", \(x, ...) standardGeneric("extent"))
 setGeneric("channels", \(x, ...) standardGeneric("channels"))
+setGeneric("centroids", \(x, ...) standardGeneric("centroids"))
 setGeneric("data_type", \(x, ...) standardGeneric("data_type"))
 setGeneric("geom_type", \(x, ...) standardGeneric("geom_type"))
-setGeneric("centroids", \(x, ...) standardGeneric("centroids"))
-setGeneric("extent", \(x, ...) standardGeneric("extent"))
+setGeneric("multiscales", \(x, ...) standardGeneric("multiscales"))
 
 # tbl ----
 
diff --git a/R/CTgraph.R b/R/CTgraph.R
index ee47ebd3..a1a2dd40 100644
--- a/R/CTgraph.R
+++ b/R/CTgraph.R
@@ -10,6 +10,19 @@
 #' @param fac,max scalar numeric; node labels with \code{nchar>max}
 #'   are split and hyphenated at position \code{floor(nchar/fac)}
 #' 
+#' @returns
+#' \itemize{
+#' \item \code{CTgraph}: 
+#'   \code{graph::graphAM} object with nodes for each element and
+#'   coordinate space, and edges for each transformation (if specified)
+#' \item \code{CTpath}: 
+#'   list of transformations from \code{i} to \code{j};
+#'   length > 1 if \code{type} is \code{"sequential"}, length-1 otherwise;
+#'   each element specifies \code{type} and \code{data} of the transformation
+#' \item \code{CTplot}: 
+#'   visualizes the element-coordinate space graph with \code{Rgraphviz}
+#' }
+#' 
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
 #' x <- system.file(x, package="SpatialData")
diff --git a/R/coord_utils.R b/R/CTutils.R
similarity index 79%
rename from R/coord_utils.R
rename to R/CTutils.R
index 91a1517b..124c0929 100644
--- a/R/coord_utils.R
+++ b/R/CTutils.R
@@ -1,17 +1,34 @@
-#' @name coord-utils
-#' @title Coordinate transformations
+#' @name CTutils
+#' @title Coord. trans. utilities
 #' @aliases axes CTlist CTname CTtype CTdata addCT rmvCT
 #' 
 #' @param x \code{SpatialData}, an element, or \code{Zattrs}.
 #' @param i for \code{CTpath}, source node label; else, string or 
 #'   scalar integer giving the name or index of a coordinate space.
-#' @param j character string; name of target coordinate space.
 #' @param name character(1); name of coordinate space
 #' @param type character(1); type of transformation
 #' @param data transformation data; size and shape depend on transformation and
 #'   element type (e.g., numeric(1) for rotation, numeric(2) for scaling in 2D)
 #' @param ... option arguments passed to and from other methods.
 #' 
+#' @returns
+#' \itemize{
+#' \item \code{CTname}: character string; 
+#'   transformation name (e.g., "global")
+#' \item \code{CTtype}: character string; 
+#'   transformation type (e.g., "affine")
+#' \item \code{CTdata}: list;
+#'   transformation data (e.g., scalar numeric for rotation)
+#' \item \code{CTlist}: list;
+#'   list of transformation specifications per OME-NGFF spec
+#' \item \code{add/rmvCT}: 
+#'   \code{SpatialDataElement} or \code{Zattrs} 
+#'   with transformation(s) added/removed
+#' \item \code{axes}: list; 
+#'   each element is a character string (name), or list 
+#'   with axis name and type (e.g., "space" or "channel")
+#' }
+#' 
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
 #' x <- system.file(x, package="SpatialData")
@@ -38,30 +55,31 @@ NULL
 
 # axes() ----
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("axes", "Zattrs", \(x, ...) {
-    if (!is.null(ms <- x$multiscales)) x <- ms[[1]]
+    ms <- multiscales(x)
+    if (!is.null(ms)) x <- ms[[1]]
     if (is.null(x <- x$axes)) stop("couldn't find 'axes'") 
     return(x)
 })
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("axes", "SpatialDataElement", \(x, ...) axes(meta(x)))
 
 # CTlist/data/type/name() ----
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTlist", "Zattrs", \(x, ...) {
-    ms <- "multiscales"
+    ms <- multiscales(x)
     ct <- "coordinateTransformations"
-    if (is.null(x[[ms]])) return(x[[ct]])
-    x[[ms]][[1]][[ct]]
+    if (is.null(ms)) return(x[[ct]])
+    ms[[1]][[ct]]
 })
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTdata", "Zattrs", \(x, i=1, ...) {
     stopifnot(length(i) == 1)
@@ -81,31 +99,35 @@ setMethod("CTdata", "Zattrs", \(x, i=1, ...) {
     mapply(x=ts, i=names(ts), \(x, i) x[[i]], SIMPLIFY=FALSE)
 })
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
-setMethod("CTtype", "Zattrs", \(x, ...) vapply(CTlist(x), \(.) .$type, character(1)))
+setMethod("CTtype", "Zattrs", \(x, ...) {
+    vapply(CTlist(x), \(.) .$type, character(1))
+})
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
-setMethod("CTname", "Zattrs", \(x, ...) vapply(CTlist(x), \(.) .$output$name, character(1)))
+setMethod("CTname", "Zattrs", \(x, ...) {
+    vapply(CTlist(x), \(.) .$output$name, character(1))
+})
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTlist", "SpatialDataElement", \(x, ...) CTlist(meta(x)))
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTdata", "SpatialDataElement", \(x, i=1, ...) CTdata(meta(x), i))
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTtype", "SpatialDataElement", \(x, ...) CTtype(meta(x)))
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTname", "SpatialDataElement", \(x, ...) CTname(meta(x)))
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("CTname", "SpatialData", \(x, ...) {
     g <- CTgraph(x)
@@ -115,12 +137,12 @@ setMethod("CTname", "SpatialData", \(x, ...) {
 
 # rmv ----
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("rmvCT", "SpatialDataElement", 
     \(x, i) { x@meta <- rmvCT(meta(x), i); x })
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("rmvCT", "Zattrs", \(x, i) {
     nms <- CTname(x)
@@ -155,7 +177,7 @@ setMethod("rmvCT", "Zattrs", \(x, i) {
 
 # add ----
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("addCT", "SpatialDataElement", \(x, name, type, data) {
     x@meta <- addCT(meta(x), name, type, data); x })
@@ -173,7 +195,7 @@ setMethod("addCT", "SpatialDataElement", \(x, name, type, data) {
     if (!.) f(t)
 }
 
-#' @rdname coord-utils
+#' @rdname CTutils
 #' @export
 setMethod("addCT", "Zattrs", \(x, name, type="identity", data=NULL) {
     stopifnot(
diff --git a/R/ImageArray.R b/R/ImageArray.R
index afc52939..58539966 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -31,7 +31,12 @@ ImageArray <- function(data=list(), meta=Zattrs(), metadata=list(), ...) {
 #' @rdname ImageArray
 #' @aliases channels
 #' @export
-setMethod("channels", "Zattrs", \(x, ...) unlist(x$omero$channels))
+setMethod("channels", "Zattrs", \(x, ...) {
+    v <- x$spatialdata_attrs$version
+    if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
+    if (v == "0.3") x <- x$ome
+    unlist(x$omero$channels)
+})
 
 #' @rdname ImageArray
 #' @aliases channels
@@ -43,11 +48,11 @@ setMethod("channels", "ImageArray", \(x, ...) channels(meta(x)))
 setMethod("channels", "ANY", \(x, ...) stop("only 'images' have channels"))
 
 #' @importFrom S4Vectors isSequence
-.get_multiscales_dataset_paths <- function(md) {
+.get_multiscales_dataset_paths <- function(za) {
     # validate 'multiscales'
-    .validate_multiscales_dataset_path(md)
+    ms <- .check_ms(za)
     # get & validate 'path's
-    ds <- md$multiscales[[1]]$datasets
+    ds <- ms[[1]]$datasets
     ps <- vapply(ds, \(.) .$path, character(1))
     ps <- suppressWarnings(as.numeric(sort(ps, decreasing=FALSE)))
     if (length(ps)) {
@@ -59,10 +64,9 @@ setMethod("channels", "ANY", \(x, ...) stop("only 'images' have channels"))
     return(ps)
 }
 
-#' @noRd
-.validate_multiscales_dataset_path <- function(md) {
-    # validate 'multiscales' 
-    ms <- md$multiscales
+.check_ms <- \(za) {
+    # validate 'multiscales'
+    ms <- multiscales(za)
     if (!is.null(ms)) {
         # validate 'datasets' 
         ds <- ms[[1]]$datasets
@@ -78,6 +82,7 @@ setMethod("channels", "ANY", \(x, ...) stop("only 'images' have channels"))
     } else stop( 
         "'ImageArray' paths are ill-defined,",
         " no 'multiscales' attribute under '.zattrs'")
+    return(ms)
 }
 
 .check_jk <- \(x, .) {
diff --git a/R/LabelArray.R b/R/LabelArray.R
index 403f8b3f..0f544ba9 100644
--- a/R/LabelArray.R
+++ b/R/LabelArray.R
@@ -25,7 +25,13 @@
 #' @return \code{LabelArray}
 #'
 #' @examples
-#' # TODO
+#' x <- file.path("extdata", "blobs.zarr")
+#' x <- system.file(x, package="SpatialData")
+#' x <- file.path(x, "labels", "blobs_labels")
+#' 
+#' (y <- readLabel(x))
+#' y[1:10, 1:10]
+#' meta(y)
 #'
 #' @importFrom S4Vectors metadata<-
 #' @importFrom methods new
diff --git a/R/ShapeFrame.R b/R/ShapeFrame.R
index b8e11a51..86ad2b91 100644
--- a/R/ShapeFrame.R
+++ b/R/ShapeFrame.R
@@ -10,7 +10,7 @@
 #'   content describing the overall object.
 #' @param name character string for extraction (see \code{?base::`$`}).
 #' @param i,j indices specifying elements to extract.
-#' @param drop ignored.
+#' @param drop,pattern ignored.
 #' @param ... optional arguments passed to and from other methods.
 #'
 #' @return \code{ShapeFrame}
@@ -55,15 +55,15 @@ setMethod("names", "ShapeFrame", \(x) names(data(x)))
 #' @export
 #' @rdname ShapeFrame
 #' @importFrom utils .DollarNames
-.DollarNames.ShapeFrame <- \(x, pattern="") {
+.DollarNames.ShapeFrame <- \(x, pattern="") 
     grep(pattern, names(x), value=TRUE)
-}
 
 #' @rdname ShapeFrame
 #' @exportMethod $
 setMethod("$", "ShapeFrame", \(x, name) data(x)[[name]])
 
 #' @export
+#' @rdname ShapeFrame
 #' @importFrom sf st_as_sf st_geometry_type
 setMethod("geom_type", "ShapeFrame", \(x) {
     y <- st_as_sf(data(x[1, ]))
diff --git a/R/SpatialData.R b/R/SpatialData.R
index bacbfe6f..57ceed4a 100644
--- a/R/SpatialData.R
+++ b/R/SpatialData.R
@@ -8,6 +8,8 @@
 #' image images image<- images<- imageNames 
 #' shape shapes shape<- shapes<- shapeNames 
 #' table tables table<- tables<- tableNames 
+#' [[<-,SpatialData,character,ANY-method
+#' [[<-,SpatialData,numeric,ANY-method
 #' 
 #' @description ...
 #' 
diff --git a/R/Zattrs.R b/R/Zattrs.R
index 9bae799b..eb969bec 100644
--- a/R/Zattrs.R
+++ b/R/Zattrs.R
@@ -1,8 +1,6 @@
 #' @name Zattrs
 #' @title The `Zattrs` class
 #' 
-#' @aliases feature_key
-#' 
 #' @param x list extracted from a OME-NGFF compliant .zattrs file.
 #' @param name character string for extraction (see ?base::`$`).
 #' 
@@ -38,6 +36,14 @@ Zattrs <- \(x=list()) {
 #' @exportMethod $
 setMethod("$", "Zattrs", \(x, name) x[[name]])
 
+# internal use only!
+#' @noRd 
+setMethod("multiscales", "list", \(x) {
+    v <- x$spatialdata_attrs$version
+    if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
+    switch(v, "0.3"=x$ome$multiscales, x$multiscales)
+})
+
 .showZattrs <- function(object) {
     cat("class: Zattrs\n")
     ax <- axes(object)
@@ -80,22 +86,57 @@ setMethod("$", "Zattrs", \(x, name) x[[name]])
 }
 setMethod("show", "Zattrs", .showZattrs)
 
+#' @name SDattrs
+#' @title \code{SpatialData} attributes
+#' 
+#' @aliases
+#' region
+#' region_key
+#' feature_key
+#' instance_key
+#' 
+#' @param x depends on which attributes are available; 
+#'   specifically, \code{PointFrame} (\code{feature/instance_key}), or
+#'   \code{SingleCellExperiment} (\code{region}, \code{region/instance_key}),
+#' 
+#' @return character string
+#'
+#' @examples
+#' x <- file.path("extdata", "blobs.zarr")
+#' x <- system.file(x, package="SpatialData")
+#' x <- readSpatialData(x, anndataR=TRUE)
+#' 
+#' region(table(x))
+#' region_key(table(x))
+#' 
+#' instance_key(point(x))
+#' fk <- feature_key(point(x))
+#' base::table(point(x)[[fk]])
+NULL
+
 # TODO: only points can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("feature_key", "list", \(x) x$spatialdata_attrs$feature_key)
 #' @export
+#' @rdname SDattrs
 setMethod("feature_key", "PointFrame", \(x) feature_key(meta(x)))
 
 # TODO: only tables can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("region_key", "SingleCellExperiment", \(x) meta(x)$region_key)
 #' @export
+#' @rdname SDattrs
 setMethod("region", "SingleCellExperiment", \(x) meta(x)[[region_key(x)]])
 
 # TODO: only tables and points can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "list", \(x) x$instance_key)
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "PointFrame", \(x) instance_key(meta(x)$spatialdata_attrs))
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "SingleCellExperiment", \(x) instance_key(meta(x)))
diff --git a/R/data.R b/R/data.R
index 9c6daa62..97aa5bf2 100644
--- a/R/data.R
+++ b/R/data.R
@@ -4,7 +4,7 @@
 #' 
 #' @description data were retrieved on Nov. 11th, 2024, from \href{https://github.com/scverse/spatialdata-notebooks/tree/main/notebooks/developers_resources/storage_format/multiple_elements.zarr}{here}.
 #'
-#' @return NULL
+#' @returns zarr store.
 #'
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
diff --git a/R/misc.R b/R/misc.R
index ad128704..713a5b82 100644
--- a/R/misc.R
+++ b/R/misc.R
@@ -1,9 +1,14 @@
 #' @name misc
 #' @title Miscellaneous `SpatialData` methods
-#' @description ...
-#'
-#' @param object \code{\link{SpatialData}} object or one of its 
-#'   elements, i.e., an Image/LabelArray or Point/ShapeFrame.
+#' @aliases show,SpatialData-method
+#' 
+#' @description 
+#' Miscellaneous methods (e.g., \code{show}) for the
+#' \code{\link{SpatialData}} class and its elements.
+#' 
+#' @param object 
+#'   \code{\link{SpatialData}} object or one of its elements,
+#'   i.e., an \code{Image/LabelArray} or \code{Point/ShapeFrame}.
 #'
 #' @return \code{NULL}
 #'
diff --git a/R/query.R b/R/query.R
index f5fa6bd3..01fa1524 100644
--- a/R/query.R
+++ b/R/query.R
@@ -10,8 +10,8 @@
 #'
 #' @param x \code{SpatialData} element.
 #' @param y query specification; 
-#' bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax' 
-#' (order is irrelevant); polygon: numeric matrix with ≥ 3 rows and 2 columns.
+#' bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax';
+#' polygon: numeric matrix with at least 3 rows and exactly 2 columns.
 #' @param i for \code{SpatialData}, index or name of table to query.
 #' @param ... optional arguments passed to and from other methods.
 #'
@@ -97,8 +97,8 @@ setMethod("query", "SpatialData", \(x, ..., i) {
         nrow(mx) >= 3, ncol(mx) == 2,
         !is.na(mx), is.finite(mx))
     if (!all(ok)) stop(
-        "Invalid polygon query; should be numeric matrix ",
-        "with ≥ 3 rows and 2 columns (= xy-coordinates)")
+        "Invalid polygon query; should be numeric matrix with at ",
+        "least 3 rows and exactly 2 columns (= xy-coordinates)")
     # ensure polygon is closed
     top <- mx[1, ]
     bot <- mx[nrow(mx), ]
diff --git a/R/read.R b/R/read.R
index f0dbec78..78217254 100644
--- a/R/read.R
+++ b/R/read.R
@@ -1,4 +1,3 @@
-#
 # allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7", 
 # "pillow==11.1.0", "anndata==0.11.3", "annotated_types==0.7.0", "asciitree==0.3.3", 
 # "attr==0.3.2", "certifi==2025.01.31", "charset_normalizer==3.4.1", 
@@ -25,8 +24,14 @@
 # "typing_extensions==4.12.2", "urllib3==2.3.0", "wrapt==1.17.2", 
 # "xarray==2024.11.0", "xarray_dataclasses==1.9.1", "xarray_schema==0.0.3", 
 # "zarr==2.18.4", "zict==3.0.0")
-allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0", 
-         "spatialdata_plot==0.2.14", "setuptools==75.8.0")
+
+allp <- c(
+    "zarr==3.1.5", 
+    "spatialdata==0.7.0", 
+    "spatialdata_io==0.6.0", 
+    "spatialdata_plot==0.2.14", 
+    "setuptools==75.8.0")
+
 # notes from VJC/AM -- readSpatialData was modified below so
 # that if anndataR = FALSE, anndata.read_zarr is used
 # to get the whole zarr store, and then the tables are
@@ -34,7 +39,6 @@ allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0",
 # for ingesting the visium_hd_3.0.0 example but fails on
 # the blobs dataset in example("table-utils") because
 # of matters related to metadata/hasTable behavior
-#
 
 #' @name readSpatialData
 #' @title Reading `SpatialData`
@@ -203,8 +207,10 @@ readSpatialData <- function(x,
     args <- as.list(environment())[.LAYERS]
     skip <- vapply(args, isFALSE, logical(1))
     sd <- lapply(.LAYERS[!skip], \(i) {
-        y <- file.path(x, i)
-        j <- list.files(y, full.names=TRUE)
+        j <- list.dirs(
+            file.path(x, i), 
+            recursive=FALSE, 
+            full.names=TRUE)
         names(j) <- basename(j)
         if (!isTRUE(opt <- args[[i]])) {
             if (is.numeric(opt) && opt > (. <- length(j))) 
diff --git a/R/sdArray.R b/R/sdArray.R
index ea0e4662..2d8ce7cf 100644
--- a/R/sdArray.R
+++ b/R/sdArray.R
@@ -1,15 +1,14 @@
-#' @name Array-methods
+#' @name sdArray
 #' @title Methods for `ImageArray` and `LabelArray` class
 #' 
 #' @aliases 
+#' data_type
 #' data,ImageArray-method
 #' data,LabelArray-method
 #' dim,ImageArray-method
 #' dim,LabelArray-method
 #' length,ImageArray-method
 #' length,LabelArray-method
-#' data_type,ImageArray-method
-#' data_type,LabelArray-method
 #' 
 #' @param x \code{ImageArray} or  \code{LabelArray}
 #' @param k scalar index specifying which scale to extract.
@@ -30,7 +29,7 @@
 #' @importFrom methods new
 NULL
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("data", "sdArray", \(x, k=1) {
   if (is.null(k)) return(x@data)
@@ -41,25 +40,25 @@ setMethod("data", "sdArray", \(x, k=1) {
   stop("'k=", k, "' but only ", n, " resolution(s) available")
 })
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("dim", "sdArray", \(x) dim(data(x)))
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("length", "sdArray", \(x) length(data(x, NULL)))
 
 #' @export
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @importFrom S4Vectors metadata
 setMethod("data_type", "sdArray", \(x) {
     if (is(y <- data(x), "DelayedArray")) 
         data_type(y) else metadata(x)$data_type
 })
 
-#' @rdname Array-methods
+#' @export
+#' @rdname sdArray
 #' @importFrom DelayedArray DelayedArray
 #' @importFrom Rarr zarr_overview
 #' @importFrom ZarrArray path
-#' @export
 setMethod("data_type", "DelayedArray", \(x) zarr_overview(path(x), as_data_frame=TRUE)$data_type)
diff --git a/R/table_utils.R b/R/table_utils.R
index 784c7c47..7e2e6e59 100644
--- a/R/table_utils.R
+++ b/R/table_utils.R
@@ -18,6 +18,19 @@
 #' @param ... \code{data.frame} or list of data generation function(s) 
 #'   that accept an argument for the number of observations; see examples.
 #'   
+#' @returns 
+#' \itemize{
+#' \item \code{hasTable}: 
+#'   logical scalar (or character string, if \code{name=TRUE});
+#'   whether or not a \code{table} annotating \code{i} exists in \code{x}
+#' \item \code{getTable}: 
+#'   \code{SingleCellExperiment}; the \code{table} annotating 
+#'   \code{i} with optional filtering of matching observations
+#' \item \code{valTable}: 
+#'   vector of values (according to \code{j})
+#'   from the \code{table} annotating \code{i}
+#' }  
+#'   
 #' @examples
 #' library(SingleCellExperiment)
 #' x <- file.path("extdata", "blobs.zarr")
diff --git a/R/trans.R b/R/trans.R
index bb303385..af9ec51f 100644
--- a/R/trans.R
+++ b/R/trans.R
@@ -3,9 +3,7 @@
 #' @title Transformations
 #' @aliases scale rotate translation flip flop mirror
 #' 
-#' @param x \code{SpatialData} element
-#' @param j scalar character or numeric; 
-#'   name or index of coordinate space.
+#' @param x \code{SpatialData} element.
 #' @param t transformation data; exceptions: for \code{mirror}, controls
 #'   whether to perform \bold{v}ertical or \bold{h}orizontal reflection;
 #'   no data is needed for \code{flip} (\bold{v}) and \code{flop} (\bold{h}).
@@ -14,6 +12,8 @@
 #'   only applies to \code{sdArray}s (images, labels).
 #' @param ... option arguments passed to and from other methods.
 #' 
+#' @returns \code{SpatialData} element with transformation(s) applied.
+#' 
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
 #' x <- system.file(x, package="SpatialData")
@@ -106,6 +106,8 @@ setMethod("rotate", c("sdArray", "numeric"), \(x, t, k=1,...) {
     .trans_a(x, f, k)
 })
 
+#' @export
+#' @rdname trans
 #' @importFrom EBImage translate
 setMethod("translation", c("sdArray", "numeric"), \(x, t, k=1, ...) {
     stopifnot(length(t) == length(dim(x)), is.finite(t))
diff --git a/R/tx_to_ext.R b/R/tx_to_ext.R
index f0149435..e4421a28 100644
--- a/R/tx_to_ext.R
+++ b/R/tx_to_ext.R
@@ -21,6 +21,8 @@
 #'   can include "maintain_positioning" (logical (1)) or numerics for
 #'   target_unit_to_pixels, target_width, target_height, target_depth.
 #'   
+#' @return \code{SpatialData} object. 
+#'   
 #' @examples
 #' src <- system.file("extdata", "blobs.zarr", package="SpatialData")
 #' td <- tempfile()
diff --git a/R/utils.R b/R/utils.R
index e2706093..8618e2ad 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -3,8 +3,14 @@
 #' @title Utilities
 #' @aliases centroids extent
 #' 
-#' @param x a \code{SpatialData} element (any but image)
-#' @param as determines how results will be returned
+#' @param x a \code{SpatialData} element (any but image).
+#' @param as character string; how results should be returned.
+#' @param ... optional arguments passed to and from other methods.
+#' 
+#' @returns
+#' For \code{centroids}, a table (\code{data.frame} or \code{matrix}) 
+#' of spatial coordinates (if \code{as="list"}, split by instance);
+#' for extend, a length-2 numeric list of x- and y-ranges.
 #' 
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")
@@ -42,11 +48,13 @@ setMethod("centroids", "ANY", \(x, ...) stop("'centroids' ",
 #' @importFrom Matrix summary
 setMethod("centroids", "LabelArray", \(x, 
     as=c("data.frame", "matrix")) {
-    # TODO: should these be offset by 0.5?
     as <- match.arg(as)
     y <- data(x)
     y <- as(y, "dgCMatrix")
     i <- summary(y)
+    # flip dimensions so that columns=x, rows=y
+    # TODO: should these be offset by 0.5?
+    i[, c(1, 2)] <- i[, c(2, 1)]-0.5
     xy <- tapply(i[, -3], i[[3]], colMeans)
     xy <- do.call(rbind, xy)
     xy <- cbind(xy, as.integer(rownames(xy)))
diff --git a/R/validity.R b/R/validity.R
index edd7ba70..f30ed209 100644
--- a/R/validity.R
+++ b/R/validity.R
@@ -26,15 +26,15 @@
             ok <- !is.null(int_colData(se)[[md$instance_key]])
             if (!ok) msg <- c(msg, paste0(
                 i, "-th table missing 'instance_key' column in 'int_colData'"))
-            
+
         }
     }
     na <- setdiff(
         unlist(lapply(tables(object), \(.) if (sce(.)) region(.))),
         unlist(colnames(object)[setdiff(.LAYERS, "tables")])) # don't flip!
-    if (length(na)) 
+    if (length(na))
         msg <- c(msg, paste(
-            "table region(s) not found in any layer:", 
+            "table region(s) not found in any layer:",
             paste(sprintf("'%s'", na), collapse=", ")))
     return(msg)
 }
@@ -72,7 +72,7 @@ setValidity2("LabelArray", .validateLabelArray)
 
 .validatePointFrame <- \(object) {
     msg <- c()
-    if (!length(object)) return(msg) 
+    if (!length(object)) return(msg)
     if (!"x" %in% names(object)) msg <- c(msg, "'PointFrame' missing 'x'.")
     if (!"y" %in% names(object)) msg <- c(msg, "'PointFrame' missing 'y'.")
     return(msg)
@@ -82,7 +82,7 @@ setValidity2("PointFrame", .validatePointFrame)
 
 .validateShapeFrame <- \(object) {
     msg <- c()
-    if (!nrow(object)) return(msg) 
+    if (!nrow(object)) return(msg)
     if (!"geometry" %in% names(object)) msg <- c(msg, "'ShapeFrame' missing 'geometry'.")
     return(msg)
 }
@@ -102,10 +102,7 @@ setValidity2("ShapeFrame", .validateShapeFrame)
         if (!all(vapply(x[[.]], \(y) is(y, typ[.]), logical(1))))
             msg <- c(msg, sprintf("'%s' should be a list of '%s'", ., typ[.]))
     # TODO: validate .zattrs across all layers
-    for (y in labels(x)) {
-        msg <- c(msg, .validateLabelArray(y))
-        msg <- c(msg, .validateZattrsLabelArray(y))
-    }
+    for (y in labels(x)) msg <- c(msg, .validateLabelArray(y))
     for (y in images(x)) msg <- c(msg, .validateImageArray(y))
     for (y in points(x)) msg <- c(msg, .validatePointFrame(y))
     for (y in shapes(x)) msg <- c(msg, .validateShapeFrame(y))
@@ -116,6 +113,8 @@ setValidity2("ShapeFrame", .validateShapeFrame)
 #' @importFrom S4Vectors setValidity2
 setValidity2("SpatialData", .validateSpatialData)
 
+# TODO: version-specific .zattrs validation for all layers
+
 .validateZattrs_multiscales <- \(x, msg) {
     if (is.null(ms <- x$multiscales[[1]]))
         msg <- c(msg, "missing 'multiscales'")
diff --git a/inst/NEWS b/inst/NEWS
index 155ca6fa..18c4e5df 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -1,3 +1,9 @@
+changes in version 0.99.29
+
+- revision of Zarr version-specific .zattrs handling
+- added Zarr v3 example dataset 'inst/extdata/blobs_v3'
+- reorganization of unit tests to facilitate v3-specific testing
+
 changes in version 0.99.28
 
 - validity checks for 'table' elements
diff --git a/man/CTgraph.Rd b/man/CTgraph.Rd
index 89336782..5892ad88 100644
--- a/man/CTgraph.Rd
+++ b/man/CTgraph.Rd
@@ -40,6 +40,19 @@ CTplot(g, cex = 0.5, fac = 2, max = 10)
 \item{fac, max}{scalar numeric; node labels with \code{nchar>max}
 are split and hyphenated at position \code{floor(nchar/fac)}}
 }
+\value{
+\itemize{
+\item \code{CTgraph}: 
+  \code{graph::graphAM} object with nodes for each element and
+  coordinate space, and edges for each transformation (if specified)
+\item \code{CTpath}: 
+  list of transformations from \code{i} to \code{j};
+  length > 1 if \code{type} is \code{"sequential"}, length-1 otherwise;
+  each element specifies \code{type} and \code{data} of the transformation
+\item \code{CTplot}: 
+  visualizes the element-coordinate space graph with \code{Rgraphviz}
+}
+}
 \description{
 Coord. trans. graph
 }
diff --git a/man/coord-utils.Rd b/man/CTutils.Rd
similarity index 76%
rename from man/coord-utils.Rd
rename to man/CTutils.Rd
index 3bc530f8..a04efc4b 100644
--- a/man/coord-utils.Rd
+++ b/man/CTutils.Rd
@@ -1,7 +1,7 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/coord_utils.R
-\name{coord-utils}
-\alias{coord-utils}
+% Please edit documentation in R/CTutils.R
+\name{CTutils}
+\alias{CTutils}
 \alias{axes}
 \alias{CTlist}
 \alias{CTname}
@@ -24,7 +24,7 @@
 \alias{rmvCT,Zattrs-method}
 \alias{addCT,SpatialDataElement-method}
 \alias{addCT,Zattrs-method}
-\title{Coordinate transformations}
+\title{Coord. trans. utilities}
 \usage{
 \S4method{axes}{Zattrs}(x, ...)
 
@@ -70,11 +70,27 @@ scalar integer giving the name or index of a coordinate space.}
 
 \item{data}{transformation data; size and shape depend on transformation and
 element type (e.g., numeric(1) for rotation, numeric(2) for scaling in 2D)}
-
-\item{j}{character string; name of target coordinate space.}
+}
+\value{
+\itemize{
+\item \code{CTname}: character string; 
+  transformation name (e.g., "global")
+\item \code{CTtype}: character string; 
+  transformation type (e.g., "affine")
+\item \code{CTdata}: list;
+  transformation data (e.g., scalar numeric for rotation)
+\item \code{CTlist}: list;
+  list of transformation specifications per OME-NGFF spec
+\item \code{add/rmvCT}: 
+  \code{SpatialDataElement} or \code{Zattrs} 
+  with transformation(s) added/removed
+\item \code{axes}: list; 
+  each element is a character string (name), or list 
+  with axis name and type (e.g., "space" or "channel")
+}
 }
 \description{
-Coordinate transformations
+Coord. trans. utilities
 }
 \examples{
 x <- file.path("extdata", "blobs.zarr")
diff --git a/man/LabelArray.Rd b/man/LabelArray.Rd
index 0c3dea1b..338f60fd 100644
--- a/man/LabelArray.Rd
+++ b/man/LabelArray.Rd
@@ -41,6 +41,12 @@ Currently defined methods (here, \code{x} is a \code{LabelArray}):
 }
 }
 \examples{
-# TODO
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+x <- file.path(x, "labels", "blobs_labels")
+
+(y <- readLabel(x))
+y[1:10, 1:10]
+meta(y)
 
 }
diff --git a/man/SDattrs.Rd b/man/SDattrs.Rd
new file mode 100644
index 00000000..c5cb65ae
--- /dev/null
+++ b/man/SDattrs.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Zattrs.R
+\name{SDattrs}
+\alias{SDattrs}
+\alias{region}
+\alias{region_key}
+\alias{feature_key}
+\alias{instance_key}
+\alias{feature_key,list-method}
+\alias{feature_key,PointFrame-method}
+\alias{region_key,SingleCellExperiment-method}
+\alias{region,SingleCellExperiment-method}
+\alias{instance_key,list-method}
+\alias{instance_key,PointFrame-method}
+\alias{instance_key,SingleCellExperiment-method}
+\title{\code{SpatialData} attributes}
+\usage{
+\S4method{feature_key}{list}(x)
+
+\S4method{feature_key}{PointFrame}(x)
+
+\S4method{region_key}{SingleCellExperiment}(x)
+
+\S4method{region}{SingleCellExperiment}(x)
+
+\S4method{instance_key}{list}(x)
+
+\S4method{instance_key}{PointFrame}(x)
+
+\S4method{instance_key}{SingleCellExperiment}(x)
+}
+\arguments{
+\item{x}{depends on which attributes are available; 
+specifically, \code{PointFrame} (\code{feature/instance_key}), or
+\code{SingleCellExperiment} (\code{region}, \code{region/instance_key}),}
+}
+\value{
+character string
+}
+\description{
+\code{SpatialData} attributes
+}
+\examples{
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+x <- readSpatialData(x, anndataR=TRUE)
+
+region(table(x))
+region_key(table(x))
+
+instance_key(point(x))
+fk <- feature_key(point(x))
+base::table(point(x)[[fk]])
+}
diff --git a/man/ShapeFrame.Rd b/man/ShapeFrame.Rd
index 8eaa3eb3..e69d3efc 100644
--- a/man/ShapeFrame.Rd
+++ b/man/ShapeFrame.Rd
@@ -8,6 +8,7 @@
 \alias{names,ShapeFrame-method}
 \alias{.DollarNames.ShapeFrame}
 \alias{$,ShapeFrame-method}
+\alias{geom_type,ShapeFrame-method}
 \alias{[,ShapeFrame,missing,ANY,ANY-method}
 \alias{[,ShapeFrame,ANY,missing,ANY-method}
 \alias{[,ShapeFrame,missing,missing,ANY-method}
@@ -26,6 +27,8 @@ ShapeFrame(data = data.frame(), meta = Zattrs(), metadata = list(), ...)
 
 \S4method{$}{ShapeFrame}(x, name)
 
+\S4method{geom_type}{ShapeFrame}(x)
+
 \S4method{[}{ShapeFrame,missing,ANY,ANY}(x, i, j, ..., drop = TRUE)
 
 \S4method{[}{ShapeFrame,ANY,missing,ANY}(x, i, j, ..., drop = TRUE)
@@ -51,7 +54,7 @@ content describing the overall object.}
 
 \item{i, j}{indices specifying elements to extract.}
 
-\item{drop}{ignored.}
+\item{drop, pattern}{ignored.}
 }
 \value{
 \code{ShapeFrame}
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index 5c16f970..913adda8 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -34,6 +34,8 @@
 \alias{table<-}
 \alias{tables<-}
 \alias{tableNames}
+\alias{[[<-,SpatialData,character,ANY-method}
+\alias{[[<-,SpatialData,numeric,ANY-method}
 \alias{$,SpatialData-method}
 \alias{[[,SpatialData,numeric,ANY-method}
 \alias{[[,SpatialData,character,ANY-method}
diff --git a/man/Zattrs.Rd b/man/Zattrs.Rd
index 06ddea16..49a06fae 100644
--- a/man/Zattrs.Rd
+++ b/man/Zattrs.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/Zattrs.R
 \name{Zattrs}
 \alias{Zattrs}
-\alias{feature_key}
 \alias{$,Zattrs-method}
 \title{The `Zattrs` class}
 \usage{
diff --git a/man/blobs.Rd b/man/blobs.Rd
index 1aad2796..9cd4b024 100644
--- a/man/blobs.Rd
+++ b/man/blobs.Rd
@@ -3,6 +3,9 @@
 \name{blobs}
 \alias{blobs}
 \title{`SpatialData` .zarr toy datasets}
+\value{
+zarr store.
+}
 \description{
 data were retrieved on Nov. 11th, 2024, from \href{https://github.com/scverse/spatialdata-notebooks/tree/main/notebooks/developers_resources/storage_format/multiple_elements.zarr}{here}.
 }
diff --git a/man/do_tx_to_ext.Rd b/man/do_tx_to_ext.Rd
index da7c529f..47c8656c 100644
--- a/man/do_tx_to_ext.Rd
+++ b/man/do_tx_to_ext.Rd
@@ -17,6 +17,9 @@ do_tx_to_ext(srcdir, dest, coordinate_system, ...)
 can include "maintain_positioning" (logical (1)) or numerics for
 target_unit_to_pixels, target_width, target_height, target_depth.}
 }
+\value{
+\code{SpatialData} object.
+}
 \description{
 Use Python's 'spatialdata' 'transform_to_data_extent' on a spatialdata zarr store
 }
diff --git a/man/misc.Rd b/man/misc.Rd
index a67f7ec8..4c5cade5 100644
--- a/man/misc.Rd
+++ b/man/misc.Rd
@@ -17,14 +17,15 @@
 \S4method{show}{ShapeFrame}(object)
 }
 \arguments{
-\item{object}{\code{\link{SpatialData}} object or one of its 
-elements, i.e., an Image/LabelArray or Point/ShapeFrame.}
+\item{object}{\code{\link{SpatialData}} object or one of its elements,
+i.e., an \code{Image/LabelArray} or \code{Point/ShapeFrame}.}
 }
 \value{
 \code{NULL}
 }
 \description{
-...
+Miscellaneous methods (e.g., \code{show}) for the
+\code{\link{SpatialData}} class and its elements.
 }
 \examples{
 zs <- file.path("extdata", "blobs.zarr")
diff --git a/man/query.Rd b/man/query.Rd
index 83d23cf4..4b566bcc 100644
--- a/man/query.Rd
+++ b/man/query.Rd
@@ -27,8 +27,8 @@
 \item{i}{for \code{SpatialData}, index or name of table to query.}
 
 \item{y}{query specification; 
-bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax' 
-(order is irrelevant); polygon: numeric matrix with ≥ 3 rows and 2 columns.}
+bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax';
+polygon: numeric matrix with at least 3 rows and exactly 2 columns.}
 }
 \value{
 same as input
diff --git a/man/Array-methods.Rd b/man/sdArray.Rd
similarity index 90%
rename from man/Array-methods.Rd
rename to man/sdArray.Rd
index 2be1a08a..cb1ca718 100644
--- a/man/Array-methods.Rd
+++ b/man/sdArray.Rd
@@ -1,15 +1,14 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sdArray.R
-\name{Array-methods}
-\alias{Array-methods}
+\name{sdArray}
+\alias{sdArray}
+\alias{data_type}
 \alias{data,ImageArray-method}
 \alias{data,LabelArray-method}
 \alias{dim,ImageArray-method}
 \alias{dim,LabelArray-method}
 \alias{length,ImageArray-method}
 \alias{length,LabelArray-method}
-\alias{data_type,ImageArray-method}
-\alias{data_type,LabelArray-method}
 \alias{data,sdArray-method}
 \alias{dim,sdArray-method}
 \alias{length,sdArray-method}
diff --git a/man/table-utils.Rd b/man/table-utils.Rd
index b83b2f8c..c9f700ee 100644
--- a/man/table-utils.Rd
+++ b/man/table-utils.Rd
@@ -56,6 +56,19 @@ or row name to retrieve \code{assay} data.}
 \item{assay}{character string or scalar integer; 
 specifies which \code{assay} to use when \code{j} is a row name.}
 }
+\value{
+\itemize{
+\item \code{hasTable}: 
+  logical scalar (or character string, if \code{name=TRUE});
+  whether or not a \code{table} annotating \code{i} exists in \code{x}
+\item \code{getTable}: 
+  \code{SingleCellExperiment}; the \code{table} annotating 
+  \code{i} with optional filtering of matching observations
+\item \code{valTable}: 
+  vector of values (according to \code{j})
+  from the \code{table} annotating \code{i}
+}
+}
 \description{
 \code{SpatialData} annotations
 }
diff --git a/man/trans.Rd b/man/trans.Rd
index 4378d4eb..b4f9c87d 100644
--- a/man/trans.Rd
+++ b/man/trans.Rd
@@ -13,6 +13,7 @@
 \alias{flop,sdArray-method}
 \alias{scale,sdArray,numeric-method}
 \alias{rotate,sdArray,numeric-method}
+\alias{translation,sdArray,numeric-method}
 \alias{scale,PointFrame,numeric-method}
 \alias{rotate,PointFrame,numeric-method}
 \alias{translation,PointFrame,numeric-method}
@@ -31,6 +32,8 @@
 
 \S4method{rotate}{sdArray,numeric}(x, t, k = 1, ...)
 
+\S4method{translation}{sdArray,numeric}(x, t, k = 1, ...)
+
 \S4method{scale}{PointFrame,numeric}(x, t, ...)
 
 \S4method{rotate}{PointFrame,numeric}(x, t, ...)
@@ -44,7 +47,7 @@
 \S4method{translation}{ShapeFrame,numeric}(x, t, ...)
 }
 \arguments{
-\item{x}{\code{SpatialData} element}
+\item{x}{\code{SpatialData} element.}
 
 \item{t}{transformation data; exceptions: for \code{mirror}, controls
 whether to perform \bold{v}ertical or \bold{h}orizontal reflection;
@@ -55,9 +58,9 @@ no data is needed for \code{flip} (\bold{v}) and \code{flop} (\bold{h}).}
 only applies to \code{sdArray}s (images, labels).}
 
 \item{...}{option arguments passed to and from other methods.}
-
-\item{j}{scalar character or numeric; 
-name or index of coordinate space.}
+}
+\value{
+\code{SpatialData} element with transformation(s) applied.
 }
 \description{
 Transformations
diff --git a/man/utils.Rd b/man/utils.Rd
index cc478d2b..245bc2c4 100644
--- a/man/utils.Rd
+++ b/man/utils.Rd
@@ -25,9 +25,16 @@
 \S4method{extent}{SpatialDataElement}(x)
 }
 \arguments{
-\item{x}{a \code{SpatialData} element (any but image)}
+\item{x}{a \code{SpatialData} element (any but image).}
 
-\item{as}{determines how results will be returned}
+\item{...}{optional arguments passed to and from other methods.}
+
+\item{as}{character string; how results should be returned.}
+}
+\value{
+For \code{centroids}, a table (\code{data.frame} or \code{matrix}) 
+of spatial coordinates (if \code{as="list"}, split by instance);
+for extend, a length-2 numeric list of x- and y-ranges.
 }
 \description{
 Utilities
diff --git a/tests/testthat/test-PointFrame.R b/tests/testthat/test-PointFrame.R
index d9397525..c8f089a1 100644
--- a/tests/testthat/test-PointFrame.R
+++ b/tests/testthat/test-PointFrame.R
@@ -37,7 +37,8 @@ test_that("filter", {
     n <- length(p <- point(x))
     expect_length(filter(p), n)
     expect_length(filter(p, x > Inf), 0)
-    expect_error(filter(p, z == 1))
+    f <- \() filter(p, z == 1)
+    expect_error(show(f()))
 })
 
 test_that("select", {
diff --git a/tests/testthat/test-ctgraph.R b/tests/testthat/test-ctgraph.R
new file mode 100644
index 00000000..b230d71a
--- /dev/null
+++ b/tests/testthat/test-ctgraph.R
@@ -0,0 +1,55 @@
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+x <- readSpatialData(x, anndataR=TRUE)
+
+test_that("CTgraph", {
+    # invalid
+    expect_error(CTgraph(list()))
+    expect_error(CTgraph(SpatialData::table(x)))
+    # object-wide
+    g <- CTgraph(x)
+    expect_is(g, "graph")
+    # graph should contain node for
+    # every element & transformation
+    ns <- lapply(setdiff(SpatialData:::.LAYERS, "tables"), 
+        \(l) lapply(names(x[[l]]), 
+            \(e) c(e, CTname(x[[l]][[e]]))))
+    ns <- sort(unique(unlist(ns)))
+    expect_true(all(ns %in% sort(graph::nodes(g))))
+    # element-wise
+    for (l in setdiff(SpatialData:::.LAYERS, "tables")) 
+        for (e in names(x[[l]])) {
+            y <- x[[l]][[e]]
+            g <- CTgraph(y)
+            expect_is(g, "graph")
+            expect_true("self" %in% graph::nodes(g))
+        }
+})
+
+test_that("CTpath", {
+    i <- "blobs_image"
+    y <- element(x, "images", i)
+    z <- CTpath(y, j <- CTname(y))
+    expect_identical(CTpath(x, i, j), z)
+    expect_is(z, "list")
+    expect_length(z <- z[[1]], 2)
+    expect_setequal(names(z), c("type", "data"))
+    expect_is(z$type, "character")
+    expect_length(z$type, 1)
+})
+
+test_that("CTplot", {
+    f <- function(.) {
+        tf <- tempfile(fileext=".pdf")
+        on.exit(unlink(tf))
+        pdf(tf); .; dev.off()
+        file.size(tf)
+    }
+    g <- CTgraph(x)
+    p <- f(CTplot(g))
+    expect_is(p, "numeric")
+    expect_true(p > f(plot(1)))
+    p <- f(CTplot(g, 0.1))
+    q <- f(CTplot(g, 0.9))
+    expect_true(p < q)
+})
diff --git a/tests/testthat/test-ctutils.R b/tests/testthat/test-ctutils.R
new file mode 100644
index 00000000..4f61b212
--- /dev/null
+++ b/tests/testthat/test-ctutils.R
@@ -0,0 +1,128 @@
+x <- file.path("extdata", "blobs.zarr")
+x <- system.file(x, package="SpatialData")
+x <- readSpatialData(x, anndataR=TRUE)
+
+.CTtype <- c(
+    "identity", "scale", "rotate", 
+    "translation", "affine", "sequence")
+
+test_that("CTlist", {
+    y <- CTlist(label(x))
+    expect_is(y, "list")
+    expect_length(y, 5)
+    z <- Reduce(intersect, lapply(y, names))
+    expect_setequal(z, c("input", "output", "type"))
+    z <- vapply(y, \(.) .$type, character(1))
+    expect_true(all(z %in% .CTtype))
+})
+test_that("CTdata", {
+    # invalid
+    expect_error(CTdata(label(x), ""))
+    expect_error(CTdata(label(x), 99))
+    expect_error(CTdata(label(x), Inf))
+    expect_error(CTdata(label(x), TRUE))
+    # identity
+    y <- CTdata(label(x), "global")
+    expect_null(y)
+    # scale
+    y <- CTdata(label(x), "scale")
+    expect_is(y, "list")
+    expect_length(y, 2)
+    expect_is(unlist(y), "numeric")
+    expect_true(all(unlist(y) > 0))
+    # translation
+    y <- CTdata(label(x), "translation")
+    expect_is(y, "list")
+    expect_length(y, 2)
+    expect_is(unlist(y), "numeric")
+    # affine
+    y <- CTdata(label(x), "affine")
+    expect_is(y, "list")
+    expect_length(y, 2)
+    expect_is(unlist(y), "numeric")
+    expect_true(all(unlist(y) > 0))
+    z <- vapply(y, length, integer(1))
+    expect_true(all(z == 3))
+    # sequence
+    y <- CTdata(label(x), "sequence")
+    expect_is(y, "list")
+    expect_length(y, 2)
+    expect_true(all(names(y) %in% .CTtype))
+    z <- vapply(y, length, integer(1))
+    expect_true(all(z == 2))
+})
+test_that("CTtype", {
+    y <- CTtype(label(x))
+    expect_is(y, "character")
+    expect_length(y, 5)
+    expect_true(all(y %in% .CTtype))
+})
+test_that("CTname,element", {
+    y <- CTname(label(x))
+    expect_is(y, "character")
+    expect_length(y, 5)
+    expect_true(all(nchar(y) > 0))
+    expect_true(!any(duplicated(y)))
+})
+test_that("CTname,object", {
+    y <- CTname(x)
+    expect_is(y, "character")
+    expect_true(!any(duplicated(y)))
+    y <- CTname(image(x))
+    z <- CTname(meta(image(x)))
+    expect_is(y, "character")
+    expect_length(y, 1)
+    expect_identical(y, z)
+})
+
+test_that("rmvCT", {
+    y <- label(x)
+    # invalid index/name
+    expect_error(rmvCT(y, 100))
+    expect_error(rmvCT(y, "."))
+    expect_error(rmvCT(y, c(".", CTname(y)[1])))
+    # identity is kept with a warning
+    expect_warning(z <- rmvCT(y, "global"))
+    expect_identical(CTname(z), CTname(y))
+    # by name
+    i <- sample(setdiff(CTname(y), "global"), 2) 
+    expect_identical(CTname(rmvCT(y, i)), setdiff(CTname(y), i))
+    # by index
+    i <- sample(which(CTtype(y) != "identity"), 2) 
+    expect_identical(CTname(rmvCT(y, i)), CTname(y)[-i])
+})
+
+test_that("addCT", {
+    # get 1st element from each layer
+    ls <- setdiff(SpatialData:::.LAYERS, "tables")
+    es <- lapply(ls, \(.) x[.,1][[.]][[1]])
+    .check_data <- \(z, x) {
+        expect_true("." %in% CTname(z))
+        ct <- CTlist(z)[[which(CTname(z) == ".")]]
+        expect_identical(ct[[t]][[1]], x)
+    }
+    for (y in es) {
+        t <- "identity"
+        expect_error(addCT(y, ".", t, 12345))
+        expect_silent(z <- addCT(y, ".", t, v <- NULL))
+        .check_data(z, v)
+        t <- "rotate"
+        expect_error(addCT(y, ".", t, -12345)) # negative
+        expect_error(addCT(y, ".", t, c(1,1))) # too many
+        expect_error(addCT(y, ".", t, ".")) # not a number
+        expect_silent(z <- addCT(y, ".", t, v <- 1)) 
+        .check_data(z, v)
+        t <- "scale"
+        d <- ifelse(is(y, "ImageArray"), 3, 2)
+        expect_error(addCT(y, ".", t, numeric(d))) # zeroes
+        expect_error(addCT(y, ".", t, 1+numeric(d+1))) # too many
+        expect_error(addCT(y, ".", t, character(d))) # not a number
+        expect_silent(z <- addCT(y, ".", t, v <- 1+numeric(d)))
+        .check_data(z, v)
+        t <- "translation"
+        expect_error(addCT(y, ".", t, numeric(d+1))) # too many
+        expect_error(addCT(y, ".", t, character(d))) # not a number
+        expect_silent(z <- addCT(y, ".", t, v <- numeric(d)))
+        .check_data(z, v)
+    }
+})
diff --git a/tests/testthat/test-reading.R b/tests/testthat/test-read.R
similarity index 100%
rename from tests/testthat/test-reading.R
rename to tests/testthat/test-read.R
diff --git a/tests/testthat/test-zattrs.R b/tests/testthat/test-zattrs.R
index 8321fd26..ccfc0edb 100644
--- a/tests/testthat/test-zattrs.R
+++ b/tests/testthat/test-zattrs.R
@@ -1,204 +1,51 @@
-x <- file.path("extdata", "blobs.zarr")
-x <- system.file(x, package="SpatialData")
-x <- readSpatialData(x, anndataR=TRUE)
-
-test_that("axes", {
-    # image
-    y <- axes(image(x))
-    expect_is(y, "list")
-    expect_length(y, 3)
-    # label
-    y <- axes(label(x))
-    expect_is(y, "list")
-    expect_length(y, 2)
-    # shape
-    y <- axes(shape(x))
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_equal(unlist(y), c("x", "y"))
-    # point
-    y <- axes(point(x))
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_equal(unlist(y), c("x", "y"))
-    # missing
-    y <- image(x)
-    y@meta$multiscales[[1]]$axes <- NULL
-    expect_error(axes(y))
-})
-
-.CTtype <- c("identity", "scale", "rotate", "translation", "affine", "sequence")
-
-test_that("CTlist", {
-    y <- CTlist(label(x))
-    expect_is(y, "list")
-    expect_length(y, 5)
-    z <- Reduce(intersect, lapply(y, names))
-    expect_setequal(z, c("input", "output", "type"))
-    z <- vapply(y, \(.) .$type, character(1))
-    expect_true(all(z %in% .CTtype))
-})
-test_that("CTdata", {
-    # invalid
-    expect_error(CTdata(label(x), ""))
-    expect_error(CTdata(label(x), 99))
-    expect_error(CTdata(label(x), Inf))
-    expect_error(CTdata(label(x), TRUE))
-    # identity
-    y <- CTdata(label(x), "global")
-    expect_null(y)
-    # scale
-    y <- CTdata(label(x), "scale")
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_is(unlist(y), "numeric")
-    expect_true(all(unlist(y) > 0))
-    # translation
-    y <- CTdata(label(x), "translation")
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_is(unlist(y), "numeric")
-    # affine
-    y <- CTdata(label(x), "affine")
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_is(unlist(y), "numeric")
-    expect_true(all(unlist(y) > 0))
-    z <- vapply(y, length, integer(1))
-    expect_true(all(z == 3))
-    # sequence
-    y <- CTdata(label(x), "sequence")
-    expect_is(y, "list")
-    expect_length(y, 2)
-    expect_true(all(names(y) %in% .CTtype))
-    z <- vapply(y, length, integer(1))
-    expect_true(all(z == 2))
-})
-test_that("CTtype", {
-    y <- CTtype(label(x))
-    expect_is(y, "character")
-    expect_length(y, 5)
-    expect_true(all(y %in% .CTtype))
-})
-test_that("CTname", {
-    y <- CTname(label(x))
-    expect_is(y, "character")
-    expect_length(y, 5)
-    expect_true(all(nchar(y) > 0))
-    expect_true(!any(duplicated(y)))
-})
-
-test_that("rmvCT", {
-    y <- label(x)
-    # invalid index/name
-    expect_error(rmvCT(y, 100))
-    expect_error(rmvCT(y, "."))
-    expect_error(rmvCT(y, c(".", CTname(y)[1])))
-    # identity is kept with a warning
-    expect_warning(z <- rmvCT(y, "global"))
-    expect_identical(CTname(z), CTname(y))
-    # by name
-    i <- sample(setdiff(CTname(y), "global"), 2) 
-    expect_identical(CTname(rmvCT(y, i)), setdiff(CTname(y), i))
-    # by index
-    i <- sample(which(CTtype(y) != "identity"), 2) 
-    expect_identical(CTname(rmvCT(y, i)), CTname(y)[-i])
-})
-
-test_that("addCT", {
-    # get 1st element from each layer
-    ls <- setdiff(SpatialData:::.LAYERS, "tables")
-    es <- lapply(ls, \(.) x[.,1][[.]][[1]])
-    .check_data <- \(z, x) {
-        expect_true("." %in% CTname(z))
-        ct <- CTlist(z)[[which(CTname(z) == ".")]]
-        expect_identical(ct[[t]][[1]], x)
-    }
-    for (y in es) {
-        t <- "identity"
-        expect_error(addCT(y, ".", t, 12345))
-        expect_silent(z <- addCT(y, ".", t, v <- NULL))
-        .check_data(z, v)
-        t <- "rotate"
-        expect_error(addCT(y, ".", t, -12345)) # negative
-        expect_error(addCT(y, ".", t, c(1,1))) # too many
-        expect_error(addCT(y, ".", t, ".")) # not a number
-        expect_silent(z <- addCT(y, ".", t, v <- 1)) 
-        .check_data(z, v)
-        t <- "scale"
-        d <- ifelse(is(y, "ImageArray"), 3, 2)
-        expect_error(addCT(y, ".", t, numeric(d))) # zeroes
-        expect_error(addCT(y, ".", t, 1+numeric(d+1))) # too many
-        expect_error(addCT(y, ".", t, character(d))) # not a number
-        expect_silent(z <- addCT(y, ".", t, v <- 1+numeric(d)))
-        .check_data(z, v)
-        t <- "translation"
-        expect_error(addCT(y, ".", t, numeric(d+1))) # too many
-        expect_error(addCT(y, ".", t, character(d))) # not a number
-        expect_silent(z <- addCT(y, ".", t, v <- numeric(d)))
-        .check_data(z, v)
-    }
-})
-
-test_that("CTname", {
-    y <- CTname(x)
-    expect_is(y, "character")
-    expect_true(!any(duplicated(y)))
-    y <- CTname(image(x))
-    z <- CTname(meta(image(x)))
-    expect_is(y, "character")
-    expect_length(y, 1)
-    expect_identical(y, z)
-})
-
-test_that("CTgraph", {
-    # invalid
-    expect_error(CTgraph(list()))
-    expect_error(CTgraph(SpatialData::table(x)))
-    # object-wide
-    g <- CTgraph(x)
-    expect_is(g, "graph")
-    # graph should contain node for
-    # every element & transformation
-    ns <- lapply(setdiff(SpatialData:::.LAYERS, "tables"), 
-        \(l) lapply(names(x[[l]]), 
-            \(e) c(e, CTname(x[[l]][[e]]))))
-    ns <- sort(unique(unlist(ns)))
-    expect_true(all(ns %in% sort(graph::nodes(g))))
-    # element-wise
-    for (l in setdiff(SpatialData:::.LAYERS, "tables")) 
-        for (e in names(x[[l]])) {
-            y <- x[[l]][[e]]
-            g <- CTgraph(y)
-            expect_is(g, "graph")
-            expect_true("self" %in% graph::nodes(g))
-        }
-})
-
-test_that("CTpath", {
-    i <- "blobs_image"
-    y <- element(x, "images", i)
-    z <- CTpath(y, j <- CTname(y))
-    expect_identical(CTpath(x, i, j), z)
-    expect_is(z, "list")
-    expect_length(z <- z[[1]], 2)
-    expect_setequal(names(z), c("type", "data"))
-    expect_is(z$type, "character")
-    expect_length(z$type, 1)
-})
-
-test_that("CTplot", {
-    f <- function(.) {
-        tf <- tempfile(fileext=".pdf")
-        on.exit(unlink(tf))
-        pdf(tf); .; dev.off()
-        file.size(tf)
-    }
-    g <- CTgraph(x)
-    p <- f(CTplot(g))
-    expect_is(p, "numeric")
-    expect_true(p > f(plot(1)))
-    p <- f(CTplot(g, 0.1))
-    q <- f(CTplot(g, 0.9))
-    expect_true(p < q)
-})
+z <- list(v1="blobs.zarr", v3="blobs_v3.zarr")
+
+for (v in names(z)) {
+    
+    x <- file.path("extdata", z[[v]])
+    x <- system.file(x, package="SpatialData")
+    x <- readSpatialData(x, anndataR=TRUE)
+        
+    test_that(paste0(v, "-multiscales"), {
+        y <- meta(image(x))
+        z <- multiscales(y)
+        expect_is(z, "list")
+        expect_length(z, 1)
+        y$spatialdata_attrs <- NULL
+        expect_error(multiscales(y))
+    })
+    
+    test_that(paste0(v, "-axes"), {
+        # image
+        y <- axes(image(x))
+        expect_is(y, "list")
+        expect_length(y, 3)
+        # label
+        y <- axes(label(x))
+        expect_is(y, "list")
+        expect_length(y, 2)
+        # shape
+        y <- axes(shape(x))
+        expect_is(y, "list")
+        expect_length(y, 2)
+        expect_equal(unlist(y), c("x", "y"))
+        # point
+        y <- axes(point(x))
+        expect_is(y, "list")
+        expect_length(y, 2)
+        expect_equal(unlist(y), c("x", "y"))
+        # missing
+        y <- image(x)
+        switch(v,
+            "v3"=y@meta$ome$multiscales[[1]]$axes <- NULL,
+            y@meta$multiscales[[1]]$axes <- NULL)
+        expect_error(axes(y))
+    })
+    
+    test_that(paste0(v, "-channels"), {
+        expect_error(channels(label(x)))
+        expect_silent(z <- channels(y <- image(x)))
+        expect_length(z, dim(y)[1])
+    })
+
+}
\ No newline at end of file