From 7f27f2005c19d44aec20ff880bcc5eb44fc53b55 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 18 Sep 2023 13:26:00 +0200
Subject: [PATCH 01/13] Start on Zarr reader

---
 R/ZarrReaders.R               | 66 +++++++++++++++++++++++++++++++++++
 vignettes/cytomapper_zarr.Rmd | 41 ++++++++++++++++++++++
 2 files changed, 107 insertions(+)
 create mode 100644 R/ZarrReaders.R
 create mode 100644 vignettes/cytomapper_zarr.Rmd

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
new file mode 100644
index 0000000..b8bda7b
--- /dev/null
+++ b/R/ZarrReaders.R
@@ -0,0 +1,66 @@
+#' @title Read data from ZARR files
+#' @name readZARR
+#'
+#' @description
+#' Reads in data from a ZARR file
+#'
+#' @param file
+#' @param 
+#'
+#' @return A \linkS4class{CytoImageList} object
+#' 
+#' @examples
+#' # TODO
+#'
+#' @author Nils Eling (\email{nils.eling@@dqbm.uzh.ch}),
+#'
+#' @export
+readZARR <- function(file,
+                     type = c("omengff", "spatialdata"),
+                     what = c("images", "masks"),
+                     resolution = NULL,
+                     z = 1,
+                     t = 1,
+                     fov_name = NULL) {
+    
+    # Check if file is spatialData or OME-NGFF
+    #.valid.readZARR.input(file)
+    
+    type <- match.arg(type)
+    what <- match.arg(what)
+    
+    if (type == "spatialdata") {
+        if (is.null(fov_name)) {
+            fov_name <- list.files(file.path(file, "images"))[1]
+        }
+    
+        cur_out <- lapply(fov_name, function(x){
+            
+            if (is.null(resolution)) {
+                cur_res <- list.files(file.path(file, "images", x))
+                cur_res <- cur_res[length(cur_res)]
+            }
+        
+            cur_name <- file.path(file, "images", x, cur_res)
+            
+            # Create index
+            cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
+            cur_dim <- cur_zarr$dim[[1]]
+            
+            if (length(cur_dim) == 3) {
+                cur_ind <- list(NULL, NULL, NULL)
+            } else if (length(cur_dim) == 4) {
+                cur_ind <- list(NULL, NULL, NULL, z)
+            } else if (length(cur_dim) == 5) {
+                cur_ind <- list(NULL, NULL, NULL, z, t)
+            }
+            
+            cur_arr <- read_zarr_array(cur_name, index = cur_ind)
+            cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))
+            
+            return(cur_arr)
+        })
+    
+    }
+    
+}
\ No newline at end of file
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
new file mode 100644
index 0000000..3462b59
--- /dev/null
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -0,0 +1,41 @@
+---
+title: "Zarr support for cytomapper"
+date: "`r BiocStyle::doc_date()`"
+package: "`r BiocStyle::pkg_ver('cytomapper')`"
+author:
+- name: Nils Eling
+  affiliation: 
+  - Department for Quantitative Biomedicine, University of Zurich
+  - Institute for Molecular Health Sciences, ETH Zurich
+  email: nils.eling@dqbm.uzh.ch
+output:
+    BiocStyle::html_document:
+        toc_float: yes
+bibliography: library.bib
+abstract: |
+    TODO
+vignette: |
+    %\VignetteIndexEntry{"On disk storage of images"}
+    %\VignetteEngine{knitr::rmarkdown}
+    %\VignetteEncoding{UTF-8}
+---
+
+```{r, echo=FALSE, results="hide"}
+knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE,
+                        fig.retina = 0.75, crop = NULL)
+library(BiocStyle)
+```
+
+```{r library, echo=FALSE}
+library(cytomapper)
+```
+
+# Zarr
+
+```{r}
+library(Rarr)
+
+test <- Rarr::read_zarr_array("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/images/blobs_image/0/")
+
+test <- Rarr::
+```
\ No newline at end of file

From 756fa336cf4dcc81d060924db7fdbd623d3e8f91 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 18 Sep 2023 13:33:30 +0200
Subject: [PATCH 02/13] Started on vignette

---
 vignettes/cytomapper_zarr.Rmd | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index 3462b59..9bba0da 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -33,9 +33,5 @@ library(cytomapper)
 # Zarr
 
 ```{r}
-library(Rarr)
 
-test <- Rarr::read_zarr_array("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/images/blobs_image/0/")
-
-test <- Rarr::
 ```
\ No newline at end of file

From c094bf39cbda126d5bcc2c4141c8317160989667 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 18 Sep 2023 15:28:07 +0200
Subject: [PATCH 03/13] Reading in images works

---
 DESCRIPTION                   |  2 +-
 NAMESPACE                     |  1 +
 NEWS                          |  3 ++
 R/ZarrReaders.R               | 71 ++++++++++++++++++++++++++---------
 man/readZARR.Rd               | 53 ++++++++++++++++++++++++++
 vignettes/cytomapper_zarr.Rmd |  3 +-
 6 files changed, 114 insertions(+), 19 deletions(-)
 create mode 100644 man/readZARR.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 754a25a..0eb1858 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: cytomapper
-Version: 1.13.0
+Version: 1.13.1
 Title: Visualization of highly multiplexed imaging data in R
 Description: 
     Highly multiplexed imaging acquires the single-cell expression of
diff --git a/NAMESPACE b/NAMESPACE
index 196bc41..6a338fd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(measureObjects)
 export(mergeChannels)
 export(plotCells)
 export(plotPixels)
+export(readZARR)
 export(scaleImages)
 exportClasses(CytoImageList)
 exportMethods("[<-")
diff --git a/NEWS b/NEWS
index 2f7d040..48f5c89 100644
--- a/NEWS
+++ b/NEWS
@@ -183,3 +183,6 @@ Changes in version 1.11.2 (2023-02-02):
 
 Changes in version 1.11.3 (2023-01-23):
 + loadImages: added option to read in single-channel images to multi-channel
+
+Changes in version 1.13.1 (2023-09-18):
++ readZARR function to read in images and masks from ZARR archives
diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index b8bda7b..7f12ab0 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -4,8 +4,16 @@
 #' @description
 #' Reads in data from a ZARR file
 #'
-#' @param file
-#' @param 
+#' @param file TODO
+#' @param type TODO
+#' @param what TODO
+#' @param resolution TODO
+#' @param x TODO
+#' @param y TODO
+#' @param c TODO
+#' @param z TODO
+#' @param t TODO
+#' @param fov_names TODO
 #'
 #' @return A \linkS4class{CytoImageList} object
 #' 
@@ -19,9 +27,12 @@ readZARR <- function(file,
                      type = c("omengff", "spatialdata"),
                      what = c("images", "masks"),
                      resolution = NULL,
+                     x = NULL,
+                     y = NULL,
+                     c = NULL,
                      z = 1,
                      t = 1,
-                     fov_name = NULL) {
+                     fov_names = NULL) {
     
     # Check if file is spatialData or OME-NGFF
     #.valid.readZARR.input(file)
@@ -29,30 +40,49 @@ readZARR <- function(file,
     type <- match.arg(type)
     what <- match.arg(what)
     
-    if (type == "spatialdata") {
-        if (is.null(fov_name)) {
-            fov_name <- list.files(file.path(file, "images"))[1]
-        }
-    
-        cur_out <- lapply(fov_name, function(x){
+    if (what == "images") {
+        if (type == "spatialdata") {
+            if (is.null(fov_names)) {
+                fov_names <- list.files(file.path(file, "images"))[1]
+            }
+            
+            if (is.null(resolution)) {
+                if (length(fov_names) > 1) {
+                    resolution <- lapply(file.path(file, "images", fov_names), 
+                                         function(cur_name) {
+                                             cur_res <- list.files(cur_name)
+                                             return(cur_res[length(cur_res)])
+                                         })
+                    resolution <- unlist(resolution)
+                } else {
+                    resolution <- list.files(file.path(file, "images", fov_names))
+                    resolution <- resolution[length(resolution)]
+                }
+            }
             
+            cur_names <- file.path(file, "images", fov_names, resolution)
+            
+        } else if (type == "omengff") {
             if (is.null(resolution)) {
-                cur_res <- list.files(file.path(file, "images", x))
-                cur_res <- cur_res[length(cur_res)]
+                resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
+                resolution <- resolution[length(resolution)]
             }
+            
+            cur_names <- file.path(file, resolution)
+        }
         
-            cur_name <- file.path(file, "images", x, cur_res)
+        cur_out <- lapply(cur_names, function(cur_name){
             
             # Create index
             cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
             cur_dim <- cur_zarr$dim[[1]]
             
             if (length(cur_dim) == 3) {
-                cur_ind <- list(NULL, NULL, NULL)
+                cur_ind <- list(c, y, x)
             } else if (length(cur_dim) == 4) {
-                cur_ind <- list(NULL, NULL, NULL, z)
+                cur_ind <- list(z, c, y,  x)
             } else if (length(cur_dim) == 5) {
-                cur_ind <- list(NULL, NULL, NULL, z, t)
+                cur_ind <- list(t, z, c, y, x)
             }
             
             cur_arr <- read_zarr_array(cur_name, index = cur_ind)
@@ -60,7 +90,14 @@ readZARR <- function(file,
             
             return(cur_arr)
         })
-    
+        
+        names(cur_out) <- fov_names
+        
+        cur_CIL <- CytoImageList(cur_out)
+        
+        return(cur_CIL)
+    } else if (what == "masks") {
+        
     }
-    
+
 }
\ No newline at end of file
diff --git a/man/readZARR.Rd b/man/readZARR.Rd
new file mode 100644
index 0000000..f4f263f
--- /dev/null
+++ b/man/readZARR.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ZarrReaders.R
+\name{readZARR}
+\alias{readZARR}
+\title{Read data from ZARR files}
+\usage{
+readZARR(
+  file,
+  type = c("omengff", "spatialdata"),
+  what = c("images", "masks"),
+  resolution = NULL,
+  x = NULL,
+  y = NULL,
+  c = NULL,
+  z = 1,
+  t = 1,
+  fov_names = NULL
+)
+}
+\arguments{
+\item{file}{TODO}
+
+\item{type}{TODO}
+
+\item{what}{TODO}
+
+\item{resolution}{TODO}
+
+\item{x}{TODO}
+
+\item{y}{TODO}
+
+\item{c}{TODO}
+
+\item{z}{TODO}
+
+\item{t}{TODO}
+
+\item{fov_name}{TODO}
+}
+\value{
+A \linkS4class{CytoImageList} object
+}
+\description{
+Reads in data from a ZARR file
+}
+\examples{
+# TODO
+
+}
+\author{
+Nils Eling (\email{nils.eling@dqbm.uzh.ch}),
+}
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index 9bba0da..4e34c18 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -33,5 +33,6 @@ library(cytomapper)
 # Zarr
 
 ```{r}
-
+images <- readZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
+                   type = "spatialdata", what = "images")
 ```
\ No newline at end of file

From a9ac4d04a13ed4e833b972b75f0d6dd20480d454 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 18 Sep 2023 16:56:13 +0200
Subject: [PATCH 04/13] Read in channel names

---
 NAMESPACE                     |  1 +
 R/ZarrReaders.R               | 37 +++++++++++++++++++++++++++++++++++
 man/readZARR.Rd               |  2 +-
 vignettes/cytomapper_zarr.Rmd |  3 +++
 4 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index 6a338fd..5dbff38 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -98,6 +98,7 @@ importFrom(graphics,rect)
 importFrom(graphics,strheight)
 importFrom(graphics,strwidth)
 importFrom(graphics,text)
+importFrom(jsonlite,fromJSON)
 importFrom(matrixStats,rowRanges)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 7f12ab0..e448a51 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -23,6 +23,8 @@
 #' @author Nils Eling (\email{nils.eling@@dqbm.uzh.ch}),
 #'
 #' @export
+#' @importFrom jsonlite fromJSON
+#' @importFrom Rarr read_zarr_array zarr_overview
 readZARR <- function(file,
                      type = c("omengff", "spatialdata"),
                      what = c("images", "masks"),
@@ -62,13 +64,41 @@ readZARR <- function(file,
             
             cur_names <- file.path(file, "images", fov_names, resolution)
             
+            # Read in metadata
+            cur_meta <- lapply(file.path(file, "images", fov_names),
+                               function(cur_m) {
+                                   return(fromJSON(file.path(cur_m, ".zattrs")))
+                               })
+            
+            cur_channels <- lapply(cur_meta, function(cur_m){
+                if ("omero" %in% names(cur_meta)) {
+                    return(cur_meta$omero$channels$label)
+                } else if ("channels_metadata" %in% names(cur_meta)) {
+                    return(cur_meta$channels_metadata$channels$label)
+                } 
+            })
+            
+            if (length(unique(cur_channels)) > 1) {
+                stop("Channel names need to match across images.")
+            }
+            
         } else if (type == "omengff") {
             if (is.null(resolution)) {
                 resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
                 resolution <- resolution[length(resolution)]
             }
             
+            fov_names <- sub("\\.[^.]*$", "", basename(file))
+            
             cur_names <- file.path(file, resolution)
+            
+            cur_meta <- fromJSON(file.path(file, ".zattrs"))
+            
+            if ("omero" %in% names(cur_meta)) {
+                cur_channels <- cur_meta$omero$channels$label
+            } else if ("channels_metadata" %in% names(cur_meta)) {
+                cur_channels <- cur_meta$channels_metadata$channels$label
+            } 
         }
         
         cur_out <- lapply(cur_names, function(cur_name){
@@ -95,6 +125,13 @@ readZARR <- function(file,
         
         cur_CIL <- CytoImageList(cur_out)
         
+        # Set channelNames
+        if (exists("cur_channels")) {
+            channelNames(cur_CIL) <- cur_channels
+        } else {
+            channelNames(cur_CIL) <- as.character(seq_len(dim(cur_CIL[[1]])[3]))
+        }
+        
         return(cur_CIL)
     } else if (what == "masks") {
         
diff --git a/man/readZARR.Rd b/man/readZARR.Rd
index f4f263f..bc13b82 100644
--- a/man/readZARR.Rd
+++ b/man/readZARR.Rd
@@ -36,7 +36,7 @@ readZARR(
 
 \item{t}{TODO}
 
-\item{fov_name}{TODO}
+\item{fov_names}{TODO}
 }
 \value{
 A \linkS4class{CytoImageList} object
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index 4e34c18..20fb96c 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -35,4 +35,7 @@ library(cytomapper)
 ```{r}
 images <- readZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
                    type = "spatialdata", what = "images")
+
+#images <- readZARR("~/Desktop/5514375.zarr/", 
+#                   type = "omengff", what = "images")
 ```
\ No newline at end of file

From 9c8e8458f466eb9e73ab2f7dbe48cf934ad4bcda Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 09:34:37 +0200
Subject: [PATCH 05/13] Split into two functions

---
 R/ZarrReaders.R | 160 +++++++++++++++++++++++-------------------------
 1 file changed, 77 insertions(+), 83 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index e448a51..df1e338 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -25,9 +25,8 @@
 #' @export
 #' @importFrom jsonlite fromJSON
 #' @importFrom Rarr read_zarr_array zarr_overview
-readZARR <- function(file,
+readImagesFromZARR <- function(file,
                      type = c("omengff", "spatialdata"),
-                     what = c("images", "masks"),
                      resolution = NULL,
                      x = NULL,
                      y = NULL,
@@ -42,99 +41,94 @@ readZARR <- function(file,
     type <- match.arg(type)
     what <- match.arg(what)
     
-    if (what == "images") {
-        if (type == "spatialdata") {
-            if (is.null(fov_names)) {
-                fov_names <- list.files(file.path(file, "images"))[1]
-            }
-            
-            if (is.null(resolution)) {
-                if (length(fov_names) > 1) {
-                    resolution <- lapply(file.path(file, "images", fov_names), 
-                                         function(cur_name) {
-                                             cur_res <- list.files(cur_name)
-                                             return(cur_res[length(cur_res)])
-                                         })
-                    resolution <- unlist(resolution)
-                } else {
-                    resolution <- list.files(file.path(file, "images", fov_names))
-                    resolution <- resolution[length(resolution)]
-                }
-            }
-            
-            cur_names <- file.path(file, "images", fov_names, resolution)
-            
-            # Read in metadata
-            cur_meta <- lapply(file.path(file, "images", fov_names),
-                               function(cur_m) {
-                                   return(fromJSON(file.path(cur_m, ".zattrs")))
-                               })
-            
-            cur_channels <- lapply(cur_meta, function(cur_m){
-                if ("omero" %in% names(cur_meta)) {
-                    return(cur_meta$omero$channels$label)
-                } else if ("channels_metadata" %in% names(cur_meta)) {
-                    return(cur_meta$channels_metadata$channels$label)
-                } 
-            })
-            
-            if (length(unique(cur_channels)) > 1) {
-                stop("Channel names need to match across images.")
-            }
-            
-        } else if (type == "omengff") {
-            if (is.null(resolution)) {
-                resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
+    if (type == "spatialdata") {
+        if (is.null(fov_names)) {
+            fov_names <- list.files(file.path(file, "images"))[1]
+        }
+        
+        if (is.null(resolution)) {
+            if (length(fov_names) > 1) {
+                resolution <- lapply(file.path(file, "images", fov_names), 
+                                     function(cur_name) {
+                                         cur_res <- list.files(cur_name)
+                                         return(cur_res[length(cur_res)])
+                                     })
+                resolution <- unlist(resolution)
+            } else {
+                resolution <- list.files(file.path(file, "images", fov_names))
                 resolution <- resolution[length(resolution)]
             }
-            
-            fov_names <- sub("\\.[^.]*$", "", basename(file))
-            
-            cur_names <- file.path(file, resolution)
-            
-            cur_meta <- fromJSON(file.path(file, ".zattrs"))
-            
+        }
+        
+        cur_names <- file.path(file, "images", fov_names, resolution)
+        
+        # Read in metadata
+        cur_meta <- lapply(file.path(file, "images", fov_names),
+                           function(cur_m) {
+                               return(fromJSON(file.path(cur_m, ".zattrs")))
+                           })
+        
+        cur_channels <- lapply(cur_meta, function(cur_m){
             if ("omero" %in% names(cur_meta)) {
-                cur_channels <- cur_meta$omero$channels$label
+                return(cur_meta$omero$channels$label)
             } else if ("channels_metadata" %in% names(cur_meta)) {
-                cur_channels <- cur_meta$channels_metadata$channels$label
+                return(cur_meta$channels_metadata$channels$label)
             } 
+        })
+        
+        if (length(unique(cur_channels)) > 1) {
+            stop("Channel names need to match across images.")
         }
         
-        cur_out <- lapply(cur_names, function(cur_name){
-            
-            # Create index
-            cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
-            cur_dim <- cur_zarr$dim[[1]]
-            
-            if (length(cur_dim) == 3) {
-                cur_ind <- list(c, y, x)
-            } else if (length(cur_dim) == 4) {
-                cur_ind <- list(z, c, y,  x)
-            } else if (length(cur_dim) == 5) {
-                cur_ind <- list(t, z, c, y, x)
-            }
-            
-            cur_arr <- read_zarr_array(cur_name, index = cur_ind)
-            cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))
-            
-            return(cur_arr)
-        })
+    } else if (type == "omengff") {
+        if (is.null(resolution)) {
+            resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
+            resolution <- resolution[length(resolution)]
+        }
+        
+        fov_names <- sub("\\.[^.]*$", "", basename(file))
         
-        names(cur_out) <- fov_names
+        cur_names <- file.path(file, resolution)
         
-        cur_CIL <- CytoImageList(cur_out)
+        cur_meta <- fromJSON(file.path(file, ".zattrs"))
+        
+        if ("omero" %in% names(cur_meta)) {
+            cur_channels <- cur_meta$omero$channels$label
+        } else if ("channels_metadata" %in% names(cur_meta)) {
+            cur_channels <- cur_meta$channels_metadata$channels$label
+        } 
+    }
+    
+    cur_out <- lapply(cur_names, function(cur_name){
         
-        # Set channelNames
-        if (exists("cur_channels")) {
-            channelNames(cur_CIL) <- cur_channels
-        } else {
-            channelNames(cur_CIL) <- as.character(seq_len(dim(cur_CIL[[1]])[3]))
+        # Create index
+        cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
+        cur_dim <- cur_zarr$dim[[1]]
+        
+        if (length(cur_dim) == 3) {
+            cur_ind <- list(c, y, x)
+        } else if (length(cur_dim) == 4) {
+            cur_ind <- list(z, c, y,  x)
+        } else if (length(cur_dim) == 5) {
+            cur_ind <- list(t, z, c, y, x)
         }
         
-        return(cur_CIL)
-    } else if (what == "masks") {
+        cur_arr <- read_zarr_array(cur_name, index = cur_ind)
+        cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))
         
+        return(cur_arr)
+    })
+    
+    names(cur_out) <- fov_names
+    
+    cur_CIL <- CytoImageList(cur_out)
+    
+    # Set channelNames
+    if (exists("cur_channels")) {
+        channelNames(cur_CIL) <- cur_channels
+    } else {
+        channelNames(cur_CIL) <- as.character(seq_len(dim(cur_CIL[[1]])[3]))
     }
-
+    
+    return(cur_CIL)
 }
\ No newline at end of file

From d46ac7d93a68b462ac0a4f6bd856f190d0d7cc16 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 10:35:49 +0200
Subject: [PATCH 06/13] Read in axes from metadata

---
 R/ZarrReaders.R | 40 +++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index df1e338..b3b2a9c 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -69,10 +69,10 @@ readImagesFromZARR <- function(file,
                            })
         
         cur_channels <- lapply(cur_meta, function(cur_m){
-            if ("omero" %in% names(cur_meta)) {
-                return(cur_meta$omero$channels$label)
-            } else if ("channels_metadata" %in% names(cur_meta)) {
-                return(cur_meta$channels_metadata$channels$label)
+            if ("omero" %in% names(cur_m)) {
+                return(cur_m$omero$channels$label)
+            } else if ("channels_metadata" %in% names(cur_m)) {
+                return(cur_m$channels_metadata$channels$label)
             } 
         })
         
@@ -80,6 +80,22 @@ readImagesFromZARR <- function(file,
             stop("Channel names need to match across images.")
         }
         
+        cur_channels <- unlist(unique(cur_channels))
+        
+        cur_index <- lapply(cur_meta, function(cur_m){
+            if ("coordinateTransformations" %in% names(cur_m$multiscales)) {
+                return(cur_m$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name)
+            } else {
+                return(cur_m$multiscales$axes[[1]]$name)
+            } 
+        })
+        
+        if (length(unique(cur_index)) > 1) {
+            stop("Dimensions need to match across images.")
+        }
+        
+        cur_index <- unlist(unique(cur_index))
+        
     } else if (type == "omengff") {
         if (is.null(resolution)) {
             resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
@@ -97,6 +113,12 @@ readImagesFromZARR <- function(file,
         } else if ("channels_metadata" %in% names(cur_meta)) {
             cur_channels <- cur_meta$channels_metadata$channels$label
         } 
+        
+        if ("coordinateTransformations" %in% names(cur_meta$multiscales)) {
+            return(cur_meta$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name)
+        } else {
+            return(cur_meta$multiscales$axes[[1]]$name)
+        } 
     }
     
     cur_out <- lapply(cur_names, function(cur_name){
@@ -105,13 +127,9 @@ readImagesFromZARR <- function(file,
         cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
         cur_dim <- cur_zarr$dim[[1]]
         
-        if (length(cur_dim) == 3) {
-            cur_ind <- list(c, y, x)
-        } else if (length(cur_dim) == 4) {
-            cur_ind <- list(z, c, y,  x)
-        } else if (length(cur_dim) == 5) {
-            cur_ind <- list(t, z, c, y, x)
-        }
+        cur_ind <- list(t, c, z, y, x)
+        names(cur_ind) <-  c("t", "c", "z", "y", "x")
+        cur_ind <- cur_ind[cur_index]
         
         cur_arr <- read_zarr_array(cur_name, index = cur_ind)
         cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))

From e06ca448820883f8a9e24a8df8b829767212d15c Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 10:41:58 +0200
Subject: [PATCH 07/13] Removed unneded code

---
 R/ZarrReaders.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index b3b2a9c..8ebbd5b 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -123,10 +123,6 @@ readImagesFromZARR <- function(file,
     
     cur_out <- lapply(cur_names, function(cur_name){
         
-        # Create index
-        cur_zarr <- zarr_overview(cur_name, as_data_frame = TRUE)
-        cur_dim <- cur_zarr$dim[[1]]
-        
         cur_ind <- list(t, c, z, y, x)
         names(cur_ind) <-  c("t", "c", "z", "y", "x")
         cur_ind <- cur_ind[cur_index]

From 515922c438c938d619ce8f3b042242717b8dce70 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 11:53:00 +0200
Subject: [PATCH 08/13] Fixed bugs in readImagesFromZARR for spatialData

---
 NAMESPACE                                  |  4 +++-
 R/ZarrReaders.R                            |  7 ++++---
 man/{readZARR.Rd => readImagesFromZARR.Rd} |  9 +++------
 vignettes/cytomapper_zarr.Rmd              | 17 +++++++++++------
 4 files changed, 21 insertions(+), 16 deletions(-)
 rename man/{readZARR.Rd => readImagesFromZARR.Rd} (87%)

diff --git a/NAMESPACE b/NAMESPACE
index 5dbff38..c9d507d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,7 +14,7 @@ export(measureObjects)
 export(mergeChannels)
 export(plotCells)
 export(plotPixels)
-export(readZARR)
+export(readImagesFromZARR)
 export(scaleImages)
 exportClasses(CytoImageList)
 exportMethods("[<-")
@@ -64,6 +64,8 @@ importFrom(EBImage,readImage)
 importFrom(HDF5Array,HDF5Array)
 importFrom(HDF5Array,writeHDF5Array)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Rarr,read_zarr_array)
+importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 8ebbd5b..6821eb6 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -1,12 +1,11 @@
 #' @title Read data from ZARR files
-#' @name readZARR
+#' @name readImagesFromZARR
 #'
 #' @description
 #' Reads in data from a ZARR file
 #'
 #' @param file TODO
 #' @param type TODO
-#' @param what TODO
 #' @param resolution TODO
 #' @param x TODO
 #' @param y TODO
@@ -39,7 +38,6 @@ readImagesFromZARR <- function(file,
     #.valid.readZARR.input(file)
     
     type <- match.arg(type)
-    what <- match.arg(what)
     
     if (type == "spatialdata") {
         if (is.null(fov_names)) {
@@ -121,6 +119,9 @@ readImagesFromZARR <- function(file,
         } 
     }
     
+    message("Resolution of the image: ", resolution)
+    message("Channels of the image: ", cur_channels)
+    
     cur_out <- lapply(cur_names, function(cur_name){
         
         cur_ind <- list(t, c, z, y, x)
diff --git a/man/readZARR.Rd b/man/readImagesFromZARR.Rd
similarity index 87%
rename from man/readZARR.Rd
rename to man/readImagesFromZARR.Rd
index bc13b82..de665be 100644
--- a/man/readZARR.Rd
+++ b/man/readImagesFromZARR.Rd
@@ -1,13 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ZarrReaders.R
-\name{readZARR}
-\alias{readZARR}
+\name{readImagesFromZARR}
+\alias{readImagesFromZARR}
 \title{Read data from ZARR files}
 \usage{
-readZARR(
+readImagesFromZARR(
   file,
   type = c("omengff", "spatialdata"),
-  what = c("images", "masks"),
   resolution = NULL,
   x = NULL,
   y = NULL,
@@ -22,8 +21,6 @@ readZARR(
 
 \item{type}{TODO}
 
-\item{what}{TODO}
-
 \item{resolution}{TODO}
 
 \item{x}{TODO}
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index 20fb96c..c215755 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -28,14 +28,19 @@ library(BiocStyle)
 
 ```{r library, echo=FALSE}
 library(cytomapper)
+library(zellkonverter)
 ```
 
-# Zarr
+# SpatialData
 
 ```{r}
-images <- readZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
-                   type = "spatialdata", what = "images")
+images <- readImagesFromZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
+                   type = "spatialdata")
 
-#images <- readZARR("~/Desktop/5514375.zarr/", 
-#                   type = "omengff", what = "images")
-```
\ No newline at end of file
+images <- readImagesFromZARR("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr", 
+                   type = "omengff")
+
+```
+
+
+# OME NGFF
\ No newline at end of file

From deada1587538222b3078d8670fbdc46100bb553e Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 13:24:27 +0200
Subject: [PATCH 09/13] Read metadata from zmetadata

---
 R/ZarrReaders.R | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 6821eb6..52037cc 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -40,16 +40,23 @@ readImagesFromZARR <- function(file,
     type <- match.arg(type)
     
     if (type == "spatialdata") {
+        
+        cur_meta <- fromJSON(file.path(file, "zmetadata"))
+        cur_img_meta <- str_split(names(cur_meta$metadata), "/", simplify = TRUE)
+        cur_img_meta <- cur_img_meta[cur_img_meta[,1] == "images" & !grepl("^\\.", cur_img_meta[,2]),]
+        cur_fov_names <- unique(cur_img_meta[,2])
+        
         if (is.null(fov_names)) {
-            fov_names <- list.files(file.path(file, "images"))[1]
+            fov_names <- cur_fov_names[1]
         }
         
         if (is.null(resolution)) {
             if (length(fov_names) > 1) {
                 resolution <- lapply(file.path(file, "images", fov_names), 
                                      function(cur_name) {
-                                         cur_res <- list.files(cur_name)
-                                         return(cur_res[length(cur_res)])
+                                         cur_res <- fromJSON(file.path(cur_name, ".zattrs"))
+                                         cur_res <- cur_res$multiscales$datasets[[1]]$path
+                                         return(sort(cur_res)[length(cur_res)])
                                      })
                 resolution <- unlist(resolution)
             } else {

From 007c0cb13e346186763512df1eb144b2afac7144 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 13:48:23 +0200
Subject: [PATCH 10/13] Get right resolution

---
 R/ZarrReaders.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 52037cc..5302c7a 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -60,8 +60,9 @@ readImagesFromZARR <- function(file,
                                      })
                 resolution <- unlist(resolution)
             } else {
-                resolution <- list.files(file.path(file, "images", fov_names))
-                resolution <- resolution[length(resolution)]
+                resolution <- fromJSON(file.path(file, "images", fov_names, ".zattrs"))
+                resolution <- cur_res$multiscales$datasets[[1]]$path
+                resolution <- sort(resolution)[length(resolution)]
             }
         }
         

From 9851b77fad7d27966a7f572fc0e192f1ab14e916 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 13:51:44 +0200
Subject: [PATCH 11/13] OMENGFF get resolution from file

---
 R/ZarrReaders.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 5302c7a..e417a09 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -61,7 +61,7 @@ readImagesFromZARR <- function(file,
                 resolution <- unlist(resolution)
             } else {
                 resolution <- fromJSON(file.path(file, "images", fov_names, ".zattrs"))
-                resolution <- cur_res$multiscales$datasets[[1]]$path
+                resolution <- resolution$multiscales$datasets[[1]]$path
                 resolution <- sort(resolution)[length(resolution)]
             }
         }
@@ -103,9 +103,12 @@ readImagesFromZARR <- function(file,
         cur_index <- unlist(unique(cur_index))
         
     } else if (type == "omengff") {
+        
+        cur_meta <- fromJSON(file.path(file, ".zattrs"))
+        
         if (is.null(resolution)) {
-            resolution <- list.files(file, pattern = paste(seq(0, 10), collapse = "|"))
-            resolution <- resolution[length(resolution)]
+            resolution <- cur_meta$multiscales$datasets[[1]]$path
+            resolution <- sort(resolution)[length(resolution)]
         }
         
         fov_names <- sub("\\.[^.]*$", "", basename(file))

From 6b560b90590d24216ea86771f35b1dfead4fc3cd Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 15:31:55 +0200
Subject: [PATCH 12/13] Finalized reader function

---
 NAMESPACE                     |  1 +
 R/ZarrReaders.R               | 14 +++++++++-----
 vignettes/cytomapper_zarr.Rmd | 16 +++++++++++++---
 3 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index c9d507d..dfbe136 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -111,6 +111,7 @@ importFrom(raster,as.raster)
 importFrom(rhdf5,h5delete)
 importFrom(rhdf5,h5ls)
 importFrom(stats,quantile)
+importFrom(stringr,str_split)
 importFrom(svgPanZoom,renderSvgPanZoom)
 importFrom(svgPanZoom,svgPanZoom)
 importFrom(svgPanZoom,svgPanZoomOutput)
diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index e417a09..5584b6c 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -24,6 +24,7 @@
 #' @export
 #' @importFrom jsonlite fromJSON
 #' @importFrom Rarr read_zarr_array zarr_overview
+#' @importFrom stringr str_split
 readImagesFromZARR <- function(file,
                      type = c("omengff", "spatialdata"),
                      resolution = NULL,
@@ -115,8 +116,6 @@ readImagesFromZARR <- function(file,
         
         cur_names <- file.path(file, resolution)
         
-        cur_meta <- fromJSON(file.path(file, ".zattrs"))
-        
         if ("omero" %in% names(cur_meta)) {
             cur_channels <- cur_meta$omero$channels$label
         } else if ("channels_metadata" %in% names(cur_meta)) {
@@ -124,9 +123,9 @@ readImagesFromZARR <- function(file,
         } 
         
         if ("coordinateTransformations" %in% names(cur_meta$multiscales)) {
-            return(cur_meta$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name)
+            cur_index <- cur_meta$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name
         } else {
-            return(cur_meta$multiscales$axes[[1]]$name)
+            cur_index <- cur_meta$multiscales$axes[[1]]$name
         } 
     }
     
@@ -139,8 +138,13 @@ readImagesFromZARR <- function(file,
         names(cur_ind) <-  c("t", "c", "z", "y", "x")
         cur_ind <- cur_ind[cur_index]
         
+        cur_perm <- c("x", "y", "c", "z", "t")
+        cur_perm <- match(cur_perm, cur_index)
+        cur_perm <- cur_perm[!is.na(cur_perm)]
+        
         cur_arr <- read_zarr_array(cur_name, index = cur_ind)
-        cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))
+        cur_arr <- aperm(cur_arr, cur_perm)
+        cur_arr <- Image(array(cur_arr, dim = dim(cur_arr)[seq_len(3)]))
         
         return(cur_arr)
     })
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index c215755..9ac33b7 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -33,14 +33,24 @@ library(zellkonverter)
 
 # SpatialData
 
-```{r}
+```{r, eval=FALSE}
 images <- readImagesFromZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
                    type = "spatialdata")
 
+images <- readImagesFromZARR("https://dl01.irc.ugent.be/spatial/mibitof/data.zarr/", 
+                   type = "spatialdata")
+
+```
+
+# OME NGFF
+
+```{r,eval=FALSE}
 images <- readImagesFromZARR("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr", 
                    type = "omengff")
 
-```
+images <- readImagesFromZARR("~/Desktop/5514375.zarr/", 
+                   type = "omengff", z = 10, t = 10)
 
+plotPixels(images, colour_by = c("NCAPD2", "DNA", "NEG_Dextran"))
+```
 
-# OME NGFF
\ No newline at end of file

From ec4be86ed37bfa4172ed2b6a3754b32995e30ba6 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 19 Sep 2023 16:35:49 +0200
Subject: [PATCH 13/13] First working version

---
 NAMESPACE                     |   1 +
 R/ZarrReaders.R               | 136 ++++++++++++++++++++++++++++++++++
 man/readMasksFromZARR.Rd      |  50 +++++++++++++
 vignettes/cytomapper_zarr.Rmd |  34 ++++++++-
 4 files changed, 217 insertions(+), 4 deletions(-)
 create mode 100644 man/readMasksFromZARR.Rd

diff --git a/NAMESPACE b/NAMESPACE
index dfbe136..112c8ad 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,6 +15,7 @@ export(mergeChannels)
 export(plotCells)
 export(plotPixels)
 export(readImagesFromZARR)
+export(readMasksFromZARR)
 export(scaleImages)
 exportClasses(CytoImageList)
 exportMethods("[<-")
diff --git a/R/ZarrReaders.R b/R/ZarrReaders.R
index 5584b6c..f9d18b5 100644
--- a/R/ZarrReaders.R
+++ b/R/ZarrReaders.R
@@ -160,5 +160,141 @@ readImagesFromZARR <- function(file,
         channelNames(cur_CIL) <- as.character(seq_len(dim(cur_CIL[[1]])[3]))
     }
     
+    return(cur_CIL)
+}
+
+#' @title Read data from ZARR files
+#' @name readMasksFromZARR
+#'
+#' @description
+#' Reads in data from a ZARR file
+#'
+#' @param file TODO
+#' @param type TODO
+#' @param resolution TODO
+#' @param x TODO
+#' @param y TODO
+#' @param c TODO
+#' @param z TODO
+#' @param t TODO
+#' @param fov_names TODO
+#'
+#' @return A \linkS4class{CytoImageList} object
+#' 
+#' @examples
+#' # TODO
+#'
+#' @author Nils Eling (\email{nils.eling@@dqbm.uzh.ch}),
+#'
+#' @export
+#' @importFrom jsonlite fromJSON
+#' @importFrom Rarr read_zarr_array zarr_overview
+#' @importFrom stringr str_split
+readMasksFromZARR <- function(file,
+                     type = c("omengff", "spatialdata"),
+                     resolution = NULL,
+                     x = NULL,
+                     y = NULL,
+                     c = NULL,
+                     z = 1,
+                     t = 1,
+                     fov_names = NULL) {
+    
+    # Check if file is spatialData or OME-NGFF
+    #.valid.readZARR.input(file)
+    
+    type <- match.arg(type)
+    
+    if (type == "spatialdata") {
+      
+      cur_meta <- fromJSON(file.path(file, "zmetadata"))
+      cur_points_meta <- str_split(names(cur_meta$metadata), "/", simplify = TRUE)
+      cur_points_meta <- cur_points_meta[cur_points_meta[,1] == "labels" & !grepl("^\\.", cur_points_meta[,2]),]
+      
+      cur_fov_names <- unique(cur_points_meta[,2])
+      
+      if (is.null(fov_names)) {
+            fov_names <- cur_fov_names[1]
+        }
+        
+        if (is.null(resolution)) {
+            if (length(fov_names) > 1) {
+                resolution <- lapply(file.path(file, "labels", fov_names), 
+                                     function(cur_name) {
+                                       cur_res <- fromJSON(file.path(cur_name, ".zattrs"))
+                                       cur_res <- cur_res$multiscales$datasets[[1]]$path
+                                       return(sort(cur_res)[length(cur_res)])
+                                     })
+                
+                resolution <- unlist(resolution)
+                } else {
+                resolution <- fromJSON(file.path(file, "labels", fov_names, ".zattrs"))
+                resolution <- resolution$multiscales$datasets[[1]]$path
+                resolution <- sort(resolution)[length(resolution)]
+            }
+        }
+        
+        cur_names <- file.path(file, "labels", fov_names, resolution)
+        
+        # Read in metadata
+        cur_meta <- lapply(file.path(file, "labels", fov_names),
+                           function(cur_m) {
+                               return(fromJSON(file.path(cur_m, ".zattrs")))
+                           })
+        
+        cur_index <- lapply(cur_meta, function(cur_m){
+          if ("coordinateTransformations" %in% names(cur_m$multiscales)) {
+            return(cur_m$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name)
+          } else {
+            return(cur_m$multiscales$axes[[1]]$name)
+          } 
+        })
+        
+        if (length(unique(cur_index)) > 1) {
+          stop("Dimensions need to match across images.")
+        }
+        
+        cur_index <- unlist(unique(cur_index))
+        
+    } else if (type == "omengff") {
+      
+        if (is.null(resolution)) {
+          cur_res <- fromJSON(file.path(file, "labels/Cell/.zattrs"))
+          cur_res <- cur_res$multiscales$datasets[[1]]$path
+          resolution <- cur_res[length(cur_res)]
+          resolution <- unlist(resolution)
+        }
+      
+        fov_names <- sub("\\.[^.]*$", "", basename(file))
+        
+        cur_names <- file.path(file, "labels/Cell", resolution)
+        
+        cur_meta <- fromJSON(file.path(file, "labels/Cell/.zattrs"))
+        
+        cur_index <- if ("coordinateTransformations" %in% names(cur_meta$multiscales)) {
+            cur_meta$multiscales$coordinateTransformations[[1]]$input$axes[[1]]$name
+          } else {
+            cur_meta$multiscales$axes[[1]]$name
+          } 
+    }
+    
+    message("Resolution of the image: ", resolution)
+
+    cur_out <- lapply(cur_names, function(cur_name){
+        cur_ind <- list(t, c, z, y, x)
+        names(cur_ind) <-  c("t", "c", "z", "y", "x")
+        cur_ind <- cur_ind[cur_index]
+        
+        cur_arr <- read_zarr_array(cur_name, index = cur_ind)
+        
+        cur_arr <- Image(aperm(cur_arr, rev(seq_along(dim(cur_arr)))))
+        
+        return(cur_arr)
+    })
+    
+    names(cur_out) <- fov_names
+    
+    cur_CIL <- CytoImageList(cur_out)
+    
     return(cur_CIL)
 }
\ No newline at end of file
diff --git a/man/readMasksFromZARR.Rd b/man/readMasksFromZARR.Rd
new file mode 100644
index 0000000..33a378e
--- /dev/null
+++ b/man/readMasksFromZARR.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ZarrReaders.R
+\name{readMasksFromZARR}
+\alias{readMasksFromZARR}
+\title{Read data from ZARR files}
+\usage{
+readMasksFromZARR(
+  file,
+  type = c("omengff", "spatialdata"),
+  resolution = NULL,
+  x = NULL,
+  y = NULL,
+  c = NULL,
+  z = 1,
+  t = 1,
+  fov_names = NULL
+)
+}
+\arguments{
+\item{file}{TODO}
+
+\item{type}{TODO}
+
+\item{resolution}{TODO}
+
+\item{x}{TODO}
+
+\item{y}{TODO}
+
+\item{c}{TODO}
+
+\item{z}{TODO}
+
+\item{t}{TODO}
+
+\item{fov_names}{TODO}
+}
+\value{
+A \linkS4class{CytoImageList} object
+}
+\description{
+Reads in data from a ZARR file
+}
+\examples{
+# TODO
+
+}
+\author{
+Nils Eling (\email{nils.eling@dqbm.uzh.ch}),
+}
diff --git a/vignettes/cytomapper_zarr.Rmd b/vignettes/cytomapper_zarr.Rmd
index 9ac33b7..cfcb472 100644
--- a/vignettes/cytomapper_zarr.Rmd
+++ b/vignettes/cytomapper_zarr.Rmd
@@ -28,6 +28,7 @@ library(BiocStyle)
 
 ```{r library, echo=FALSE}
 library(cytomapper)
+library(basilisk)
 library(zellkonverter)
 ```
 
@@ -37,20 +38,45 @@ library(zellkonverter)
 images <- readImagesFromZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
                    type = "spatialdata")
 
-images <- readImagesFromZARR("https://dl01.irc.ugent.be/spatial/mibitof/data.zarr/", 
+masks <- readMasksFromZARR("~/Github/spatialdata-notebooks/notebooks/developers_resources/storage_format/multiple_elements.zarr/", 
                    type = "spatialdata")
 
+mcols(images) <- mcols(masks) <- DataFrame(image = names(images))
+
+plotPixels(images, mask = masks, colour_by = c("0", "1", "2"), img_id = "image")
+
+images <- readImagesFromZARR("https://dl01.irc.ugent.be/spatial/mibitof/data.zarr/", 
+                   type = "spatialdata", resolution = "0")
+
+masks <- readMasksFromZARR("https://dl01.irc.ugent.be/spatial/mibitof/data.zarr/", 
+                   type = "spatialdata", resolution = "0")
+
+mcols(images) <- mcols(masks) <- DataFrame(image = names(images))
+
+plotPixels(images, mask = masks, colour_by = c("0", "1", "2"), img_id = "image")
 ```
 
 # OME NGFF
 
 ```{r,eval=FALSE}
 images <- readImagesFromZARR("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr", 
-                   type = "omengff")
+                   type = "omengff", resolution = "0", z = 2, t = 1)
+
+masks <- readMasksFromZARR("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr",
+                           type = "omengff", resolution = "0", z = 2, t = 1)
+
+mcols(images) <- mcols(masks) <- DataFrame(image = names(images))
+
+plotPixels(images, mask = masks, img_id = "image", colour_by = c("NCAPD2", "DNA", "NEG_Dextran"))
 
 images <- readImagesFromZARR("~/Desktop/5514375.zarr/", 
-                   type = "omengff", z = 10, t = 10)
+                   type = "omengff", resolution = "0", z = 3, t = 1)
+
+masks <- readMasksFromZARR("~/Desktop/5514375.zarr/",
+                           type = "omengff", resolution = "0", z = 3, t = 1)
+
+mcols(images) <- mcols(masks) <- DataFrame(image = names(images))
 
-plotPixels(images, colour_by = c("NCAPD2", "DNA", "NEG_Dextran"))
+plotPixels(images, mask = masks, img_id = "image", colour_by = c("NCAPD2", "DNA", "NEG_Dextran"))
 ```