From 6d710a8d8ffd48b5adcf4b498c67c3ebb073f0ad Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Fri, 7 Aug 2026 11:40:23 +0200
Subject: [PATCH 1/2] pyramid formats are introduced

---
 R/ImageArray.R           |  3 ++-
 R/utils.R                | 16 ++++++++++++++++
 vignettes/ImageArray.Rmd |  4 ++++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/R/ImageArray.R b/R/ImageArray.R
index 2d65a6f..117ccfa 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -492,7 +492,8 @@ ImageArray <- function(
   
   # create ImageArray from file path
   if (inherits(image, "character")) {
-    if (grepl(".ome.tiff$|.ome.tif$|.qptiff$|.qptif$", image)) {
+    pyramid_formats <- paste(paste0(.PYRAMID_FORMATS, "$"), collapse = "|")
+    if (grepl(pyramid_formats, image)) {
       image <- BFPath(image, series, resolution)
     } else {
       image <- read_image(image, engine = engine)
diff --git a/R/utils.R b/R/utils.R
index f034f2c..c55a045 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -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 ?
+)
diff --git a/vignettes/ImageArray.Rmd b/vignettes/ImageArray.Rmd
index e438dde..b3c7a88 100644
--- a/vignettes/ImageArray.Rmd
+++ b/vignettes/ImageArray.Rmd
@@ -240,6 +240,10 @@ 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 

From a4b058d8eac5472d0ce35d77068bcc751494937f Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Fri, 7 Aug 2026 17:36:00 +0200
Subject: [PATCH 2/2] claude fixes and version bump

---
 DESCRIPTION              | 2 +-
 NEWS.md                  | 8 ++++++++
 R/ImageArray.R           | 5 +++--
 vignettes/ImageArray.Rmd | 3 ++-
 4 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 904fa95..a1c4f12 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: 1.1.5
+Version: 1.1.6
 Authors@R: c(
     person("Artür", "Manukyan", 
 		     role=c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index b17e2e0..a623592 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -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
diff --git a/R/ImageArray.R b/R/ImageArray.R
index 117ccfa..2c741ed 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -492,8 +492,9 @@ ImageArray <- function(
   
   # create ImageArray from file path
   if (inherits(image, "character")) {
-    pyramid_formats <- paste(paste0(.PYRAMID_FORMATS, "$"), collapse = "|")
-    if (grepl(pyramid_formats, image)) {
+    pyramid_formats <- paste0(gsub("\\.", "\\\\.", .PYRAMID_FORMATS), 
+                              "$", collapse = "|")
+    if (grepl(pyramid_formats, image, ignore.case = TRUE)) {
       image <- BFPath(image, series, resolution)
     } else {
       image <- read_image(image, engine = engine)
diff --git a/vignettes/ImageArray.Rmd b/vignettes/ImageArray.Rmd
index b3c7a88..85f946a 100644
--- a/vignettes/ImageArray.Rmd
+++ b/vignettes/ImageArray.Rmd
@@ -241,7 +241,8 @@ 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)
+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