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Merged
Artur-man merged 2 commits into from
Aug 7, 2026
Merged

pyramid formats are introduced #52

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6d710a8
pyramid formats are introduced
Artur-man Aug 7, 2026
a4b058d
claude fixes and version bump
Artur-man Aug 7, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Package: ImageArray
Type: Package
Title: A framework for on-disk and in-memory image arrays
Version: 1.1.5
Version: 1.1.6
Authors@R: c(
person("Artür", "Manukyan",
role=c("aut", "cre"),
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8 changes: 8 additions & 0 deletions NEWS.md
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@@ -1,3 +1,11 @@
# ImageArray 1.1.6

## New features

* `ImageArray` function now accepts Bioformats compatible image pyramid
formats beyond ome.tiff and qptiff. See https://bio-formats.readthedocs.io/en/latest/supported-formats.html
for more information.

# ImageArray 1.1.5

## New features
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4 changes: 3 additions & 1 deletion R/ImageArray.R
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Expand Up @@ -492,7 +492,9 @@ ImageArray <- function(

# create ImageArray from file path
if (inherits(image, "character")) {
if (grepl(".ome.tiff$|.ome.tif$|.qptiff$|.qptif$", image)) {
pyramid_formats <- paste0(gsub("\\.", "\\\\.", .PYRAMID_FORMATS),
"$", collapse = "|")
if (grepl(pyramid_formats, image, ignore.case = TRUE)) {
image <- BFPath(image, series, resolution)
} else {
image <- read_image(image, engine = engine)
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16 changes: 16 additions & 0 deletions R/utils.R
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Expand Up @@ -202,3 +202,19 @@ is.sequential <- function(x) {
#' @keywords internal
#' @noRd
.TEMPLATE_SCALES <- c(c = 1, y = 1, x = 1, z = 1, t = 0.1)

#' @keywords internal
#' @noRd
.PYRAMID_FORMATS <- c(
".ome.tiff", # OME-TIFF pyramidal TIFF variants (OME-TIFF and related)
".ome.tif",
".ome.tf2",
".ome.tf8",
".ome.btf",
".svs", # Aperio SVS
".afi", # Aperio AFI
".ndpi", # Hamamatsu NDPI
".ndpis", # Hamamatsu NDPI variants
".qptiff", # CODEX ?
".qptif" # CODEX ?
)
5 changes: 5 additions & 0 deletions vignettes/ImageArray.Rmd
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Expand Up @@ -240,6 +240,11 @@ imgarray <- ImageArray(ome.tiff.file, series = 1, resolution = 1)
imgarray
```

`r Biocpkg("ImageArray")` is also capable of reading other BioFormats
compatible image formats (e.g. qptiff, svs). For more information, visit the
[Supported Formats](https://bio-formats.readthedocs.io/en/v8.3.0/supported-formats.html)
webpage of BioFormats.

# Image Transformations

`r Biocpkg("ImageArray")` provides image transformation functions that operate
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