Package 'RBioFormats'

AnnotatedImage Class

Description

Extends the Image class from the EBImage package.

Usage

AnnotatedImage(..., metadata = ImageMetadata())

## S3 method for class 'AnnotatedImage'
print(x, short = FALSE, ...)

## S4 method for signature 'AnnotatedImage'
show(object)

## S3 method for class 'AnnotatedImage'
as.Image(x)

Arguments

...	arguments passed to the Image constructor.
metadata	an ImageMetadata object containing image metadata
x	an AnnotatedImage object.
short	logical, turns off image data preview.
object	an AnnotatedImage object

Value

AnnotatedImage returns a new AnnotatedImage object.

as.Image returns an Image object.

Slots

metadata

an ImageMetadata object containing image metadata

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

See Also

AnnotatedImageList

Examples

f = mockFile(sizeX = 256, sizeY = 256)
img = read.image(f)
img

---

AnnotatedImageList Class

Description

A list of AnnotatedImage objects.

Usage

AnnotatedImageList(...)

Arguments

...	a list of AnnotatedImage objects to include in the new object.

Value

AnnotatedImageList returns a new AnnotatedImageList object.

Examples

f = mockFile(sizeX = 256, sizeY = 256, series = 2)
img = read.image(f)
img

---

Java Memory Settings

Description

Information about the Java heap space usage.

Usage

checkJavaMemory(units = "m")

Arguments

units

Units to return the size in: "k", "m" or "g"

Value

The maximum amount of memory that the JVM will attempt to use, measured in units.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

## Not run: 
## assign 4 gigabytes of heap space to the Java environment.
options( java.parameters = "-Xmx4g" )
library( "RBioFormats" )

## End(Not run)

checkJavaMemory()

---

Metadata Accessors

Description

Get and set image metadata.

Usage

coreMetadata(x, series, ...)

globalMetadata(x, series, ...)

seriesMetadata(x, series, ...)

## S4 method for signature 'ANY'
metadata(x)

## S4 method for signature 'AnnotatedImage'
metadata(x)

## S4 method for signature 'AnnotatedImageList'
metadata(x)

## S4 method for signature 'ImageMetadata'
metadata(x)

## S4 method for signature 'ImageMetadataList'
metadata(x)

## S4 replacement method for signature 'AnnotatedImage'
metadata(x) <- value

coreMetadata(y) <- value

## S4 replacement method for signature 'AnnotatedImage'
coreMetadata(y) <- value

## S4 replacement method for signature 'ImageMetadata'
coreMetadata(y) <- value

globalMetadata(y) <- value

## S4 replacement method for signature 'AnnotatedImage'
globalMetadata(y) <- value

## S4 replacement method for signature 'ImageMetadata'
globalMetadata(y) <- value

seriesMetadata(y) <- value

## S4 replacement method for signature 'AnnotatedImage'
seriesMetadata(y) <- value

## S4 replacement method for signature 'ImageMetadata'
seriesMetadata(y) <- value

Arguments

x	an AnnotatedImage, AnnotatedImageList, ImageMetadata, or ImageMetadataList object
series	series ID
...	arguments passed to grep
value	depending on the context, an ImageMetadata object or a list
y	an AnnotatedImage or ImageMetadata object

Details

The ... arguments are passed to grep called on metadata names allowing for convenient subsetting.

Value

Named list consisting of key value pairs.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

img = read.image(system.file("images", "nuclei.tif", package="EBImage"))

coreMetadata(img)

# subset for specific names

globalMetadata(img, pattern="Image")

---

Image Frames Order

Description

Get the ordering of image frames.

Usage

dimorder(x)

Arguments

x	An Image object or an array

Value

A character vector giving the dimension names.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

# sample timelapse image
f = mockFile(sizeC=2, sizeT=10)
img = read.image(f)

dimorder(img)

---

Bio-Formats FormatTools Class

Description

A utility class for format reader and writer implementations.

Usage

FormatTools

Format

An object of class jclassName of length 1.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

# List available pixel types
sapply(0:7, FormatTools$getPixelTypeString)

---

ImageMetadata and ImageMetadataList Class

Description

Formal representation of image metadata.

Usage

ImageMetadata(
  coreMetadata = NULL,
  globalMetadata = NULL,
  seriesMetadata = NULL
)

ImageMetadataList(...)

## S3 method for class 'ImageMetadata'
print(x, list.len = 5L, ...)

## S4 method for signature 'ImageMetadata'
show(object)

## S4 method for signature 'ImageMetadataList'
show(object)

## S3 method for class 'ImageMetadataList'
print(x, ...)

Arguments

coreMetadata	a list of core metadata entries
globalMetadata	a list of global metadata entries
seriesMetadata	a list of series metadata entries
...	further arguments to be passed to other methods
x	An ImageMetadata object
list.len	numeric; maximum number of metadata entries to display
object	an ImageMetadata object

Value

ImageMetadata returns a new ImageMetadata object.

ImageMetadataList returns a new ImageMetadataList object.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

f = mockFile(sizeX = 256, sizeY = 256)
img = read.image(f)
metadata(img)

---

Generate Test Images

Description

Create a mock image of specific parameters for testing.

Usage

mockFile(name = "mockfile", ...)

Arguments

name	File name.
...	File parameters; available parameters are listed below.

Details

Generates mock files of specific size or pixel type containing gradient images. The desired parameters can be provided as key value pairs to the mockFile function. For a list of available parameters see below.

Value

A character string.

Parameters

Name	Default	Description
sizeX	512	horizontal size in pixels
sizeY	512	vertical size in pixels
sizeZ	1	number of Z sections
sizeC	1	number of channels
sizeT	1	number of time points
pixelType	uint8	string specifying pixel type: int8, uint8, int16, uint16, int32, uint32, float, double
bitsPerPixel	0	number of valid bits (<= number of bits implied by pixel type)
rgb	1	number of channels that are merged together
dimOrder	XYZCT	string describing dimension order
orderCertain	true
little	true	whether or not the pixel data should be little-endian
interleaved	true	whether or not merged channels are interleaved
indexed	false	whether or not a color lookup table is present
falseColor	false	whether or not the color lookup table is just for making the image look pretty
series	1	number of series (Images)
lutLength	3	number of entries in the color lookup table

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

f = mockFile(sizeX = 256, sizeY = 256)
img = read.image(f)
img

---

R Interface to Bio-Formats

Description

Interfaces the Bio-Formats Java library.

Usage

BioFormats.version()

Value

A character string containing the Bio-Formats library version.

Functions

• BioFormats.version(): Provides the version of the Bio-Formats library embedded in the package.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

References

Bio-Formats website

Examples

BioFormats.version()

---

Read Images

Description

Read image files using the Bio-Formats library. A list of supported formats can be found on the Bio-Formats website.

Usage

read.image(
  file,
  filter.metadata = FALSE,
  proprietary.metadata = TRUE,
  normalize = TRUE,
  series,
  resolution,
  subset,
  read.metadata = TRUE
)

Arguments

file	character, file name
filter.metadata	logical, specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table
proprietary.metadata	logical, should proprietary metadata be populated to OME-XML
normalize	logical, should the original image data be mapped to the [0,1] range
series	integer vector specifying series to read; if missing all series included in the file are read
resolution	integer vector specifying resolution levels to read; if missing all levels read
subset	named list specifing image subsetting
read.metadata	logical, should image metadata be read

Value

An AnnotatedImage object or an AnnotatedImageList object in case of multi-series data.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

See Also

read.metadata for reading image metadata, read.omexml for reading image metadata as OME-XML

Examples

require(EBImage)
f = system.file("images", "sample-color.png", package="EBImage")

img = read.image(f)
img

---

Read Image Metadata

Description

Read image metadata using the Bio-Formats library. The list of supported file formats can be found on the Bio-Formats website.

Usage

read.metadata(file, filter.metadata = FALSE, proprietary.metadata = TRUE)

Arguments

file	character, file name
filter.metadata	logical, specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table
proprietary.metadata	logical, should proprietary metadata be populated to OME-XML

Value

An ImageMetadata or ImageMetadataList object.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

See Also

read.omexml for reading image metadata as OME-XML, read.image for reading image data

Examples

require(EBImage)
f = system.file("images", "nuclei.tif", package="EBImage")

metadata = read.metadata(f)
str(metadata)

---

Read OME-XML Metadata

Description

Read the OME-XML DOM tree.

Usage

read.omexml(file, filter.metadata = FALSE, proprietary.metadata = TRUE)

Arguments

file	character, file name
filter.metadata	logical, specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table
proprietary.metadata	logical, should proprietary metadata be populated to OME-XML

Value

A string containing a dumped OME-XML DOM tree.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

See Also

read.metadata for reading image metadata, read.image for reading image data

Examples

require(EBImage)
f = system.file("images", "nuclei.tif", package="EBImage")

omexml = read.omexml(f)
omexml

---

Number of Image Series

Description

Get the number of image series contained in an object.

Usage

seriesCount(x)

## S4 method for signature 'ANY'
seriesCount(x)

## S4 method for signature 'matrix'
seriesCount(x)

## S4 method for signature 'array'
seriesCount(x)

## S4 method for signature 'ImageMetadata'
seriesCount(x)

## S4 method for signature 'AnnotatedImageList'
seriesCount(x)

## S4 method for signature 'ImageMetadataList'
seriesCount(x)

Arguments

x	an images object.

Details

Image series are encoded by AnnotatedImageList or ImageMetadataList objects. Therefore, only these objects can possibly yield image series count higher than 1 while for all the rest of image objects this number is expected to be 1.

Value

The number of image series the object contains, see Details.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

Examples

f = mockFile(sizeX = 256, sizeY = 256, series = 2)
img = read.image(f)
seriesCount(img)

meta <- metadata(img)
seriesCount(meta)

---

Write Images

Description

Save image files using the Bio-Formats library. A list of supported formats can be found on the Bio-Formats website.

Usage

write.image(x, file, force = FALSE, pixelType, littleEndian)

Arguments

x	an Image or AnnotatedImage object
file	character, file name
force	logical(1), if TRUE overwrite existing file
pixelType	character(1), data type to store pixel values
littleEndian	boolean(1), pixel data endianness

Value

File path to file is returned invisibly.

Author(s)

Andrzej Oleś <[email protected]>, 2014-2023

See Also

read.image for reading images.

Examples

f = mockFile(sizeX = 256, sizeY = 256)
img = read.image(f)

tempfile = tempfile("", , ".png")
write.image(img, tempfile)

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