Package 'romeo'

Subset an ome-zarr object

Description

Subset operation is applied on all levels of the multiscale ome-zarr object. The result is an ome-zarr object with the same number of levels, but each level is subsetted according to the provided indices.

Usage

## S3 method for class 'ome_zarr'
x[...]

Arguments

x	An ome-zarr object.
...	Indices to subset the ome-zarr object.

Details

The first image is subsetted using the provided indices, and the resulting dimensions are used to subset the remaining levels, while conserving the same scaling factor across levels

Value

A subset of an object of ome_zarr (OME-Zarr) class representing an image or label pyramid.

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
x <- ome_read(td)
y <- x[1:5,1:5]
plot(y, level = 2)

---

Extract specific levels from a multiscale ome-zarr object

Description

Extract specific levels from a multiscale ome-zarr object

Usage

extract_levels(x, levels)

Arguments

x	An ome-zarr object.
levels	Integer vector specifying the levels to extract.

Value

• If levels is of length 1, an array

• If levels is of length more than 1, an ome-zarr object

An object of ome_zarr (OME-Zarr) class representing an image or label pyramid.

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
x <- ome_read(td)
extract_levels(x, c(1, 3))
extract_levels(x, 2)

---

Read a multiscale OME-Zarr file

Description

Read a multiscale OME-Zarr file

Usage

ome_read(path, s3_client = NULL, lazy = TRUE, validate = TRUE)

Arguments

path	Path to the OME-Zarr file.
s3_client	Object created by paws.storage::s3(). Only required for a file on S3. Leave as NULL for a file on local storage.
lazy	Logical. If TRUE (the default), use ZarrArray to read data lazily. If FALSE, read data into memory using Rarr. If the data can fit into memory, setting lazy = FALSE may result in better performance.
validate	Logical.If TRUE (the default), validate the OME-Zarr file.

Value

An object of ome_zarr (OME-Zarr) class representing an image or label pyramid.

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
x <- ome_read(td)

---

Validate a multiscale OME-Zarr file

Description

Validate a multiscale OME-Zarr file

Usage

ome_validate(path, s3_client = NULL)

Arguments

path	Path to the OME-Zarr file.
s3_client	Object created by paws.storage::s3(). Only required for a file on S3. Leave as NULL for a file on local storage.

Value

This function is used for its side-effect and will return the type of the OME-Zarr schema (image, label), otherwise will invoke an error when passed an invalid OME-Zarr file

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
ome_validate(td)

---

Write a multiscale OME-Zarr file

Description

Writes an ome image to the zarr path according to ome-zarr specification

Usage

ome_write(
  image,
  path = "/",
  axes = NULL,
  scalefactors = c(2, 2, 2, 2),
  version = c("0.5", "0.4"),
  storage_options = NULL,
  type = c("image", "label"),
  label_name = NULL,
  label_metadata = NULL
)

## S4 method for signature 'array'
ome_write(
  image,
  path = "/",
  axes = NULL,
  scalefactors = c(2, 2, 2, 2),
  version = c("0.5", "0.4"),
  storage_options = NULL,
  type = c("image", "label"),
  label_name = NULL,
  label_metadata = NULL
)

## S4 method for signature 'Image'
ome_write(
  image,
  path = "/",
  axes = NULL,
  scalefactors = c(2, 2, 2, 2),
  version = c("0.5", "0.4"),
  storage_options = NULL,
  type = c("image", "label"),
  label_name = NULL,
  label_metadata = NULL
)

Arguments

image	an n-dimensional (or a path to an) array representing the image data (1<n<6)
path	the path to writing ome.zarr
axes	a character vector specifying the axes of the image (e.g. c("t", "c", "z", "y", "x"))
scalefactors	Scale factors to apply to construct a multiscale image. Importantly, each scale factor is relative to the previous scale factor. For example, if the scale factors are c(2, 2, 2), the returned multiscale image will have 4 scales.
version	OME-Zarr version (0.4 or 0.5), lower versions are not supported for writing.
storage_options	a list of storage options for the zarr array (e.g. chunks)
type	The type of OME pyramid written: 'image' (default) or 'label'.
label_name	The name of the label data.
label_metadata	label metadata added to attributes.

Value

An object of ome_zarr (OME-Zarr) class representing an image or label pyramid.

Examples

library(EBImage)
nuc <- readImage(system.file("images", "nuclei.tif", package="EBImage"))
nuc <- getFrames(nuc)[[1]]
td <- tempfile(fileext = ".ome.zarr")

# write image pyramid
ome_nuc <- ome_write(nuc,
                     path = td,
                     version = "0.4",
                     storage_options = list(chunk_dim = c(64,64)))

# nuclei segmentation using otsu's method
nuc_th = nuc > otsu(nuc)

# write label pyramid
ome_nuc_th <- ome_write(nuc_th,
                        path = td,
                        version = "0.4",
                        scalefactors = c(2,2,3),
                        storage_options = list(chunk_dim = c(64,64)),
                        label_name = "nuclei_segmentation",
                        type = "label")

---

Plot an ome_zarr object.

Description

Plot an ome_zarr object.

Usage

## S3 method for class 'ome_zarr'
plot(x, level = 1, ...)

Arguments

x	An ome_zarr object.
level	Integer. The scale level to plot. Defaults to 1 (the highest resolution).
...	Additional arguments passed to plot().

Value

None

Examples

omezarrzip <- system.file("extdata",
                          "test_ngff_image_v04.ome.zarr.zip",
                          package = "romeo")
dir.create(td <- tempfile())
unzip(omezarrzip, exdir = td)
x <- ome_read(td)
plot(x)
plot(x, 2)
plot(x, all = TRUE)

---