CardinalIO: Parsing and writing imzML files
Revised: August 12, 2023
Contents
1 Introduction
CardinalIO provides fast and efficient parsing and writing of imzML files for storage of mass spectrometry (MS) imaging experiments. It is intended to take over all file importing and exporting duties for the Cardinal package for MS imaging data analysis. Only the most basic methods are provided here. Support for higher-level objects (e.g., MSImagingExperiment from Cardinal) should provided in their respective packages.
The imzML format is an open standard for long-term storage of MS imaging experimental data. Each MS imaging dataset is composed of two files: (1) an XML metadata file ending in “.imzML” that contains experimental metadata and (2) a binary data file ending in “.ibd” that contains the actual m/z and intensity arrays. The files are linked by a UUID. Both files must be present to successfully import an MS imaging dataset.
The imzML specification is described in detail here along with example data files (two of which are included in this package). Software tools for converting vendor formats to imzML can be found here. A Java-based imzML validator is available here. A web-based imzML validator is available here.
2 Installation
CardinalIO can be installed via the BiocManager package.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CardinalIO")The same function can be used to update CardinalIO and other Bioconductor packages.
Once installed, CardinalIO can be loaded with library():
library(CardinalIO)## Loading required package: matter## Loading required package: BiocParallel## Loading required package: Matrix## Loading required package: ontologyIndex3 Structure of imzML files
Valid imzML datasets are composed of two files (“.imzML” and “.ibd”) and come in two types: “continuous” and “processed”.
3.1 XML
The XML (“.imzML”) file contains only human-readable experimental metadata in a structured plain text format using a controlled vocabulary. It can include many experimental details including sample preparation, instrument configuration, scan settings, etc. Note that a imzML file is also a valid mzML file, with additional requirements and constraints to accomodate the imaging modality.
3.2 Binary
The binary data (“.ibd”) file contains the binary m/z and intensity arrays. The structure of these files is defined by metadata in the XML file. Two arrangements of the internal binary data arrays are possible depending on the type of imzML file (“continuous” or “processed”).
A visualization of the imzML format as described below
3.3 Continuous
For “continuous” imzML files, all mass spectra share the same m/z values. Therefore, the m/z array is stored only once in the binary data file.
3.4 Processed
For “processed” imzML files, each mass spectrum has its own unique set of m/z values. Therefore, each m/z array is stored with its corresponding intensity array. This format is common for high mass resolution experiments where it would be prohibitive to store the complete profile spectrum, so the profile spectra are stored sparsely.
3.5 Additional notes
Note that both imzML types may contain either profile or centroided spectra. The spectrum representation should be specified in the imzML metadata file. Further note that despite the name, the “processed” type does not imply that any spectral processing has been performed beyond basic processing performed by the instrument.
4 Parsing imzML files
Parsing imzML files is performed with parseImzML().
path <- exampleImzMLFile("continuous")
path## [1] "/tmp/RtmpDRqzOc/Rinst2af5e73b561a25/CardinalIO/extdata/Example_Continuous_imzML1.1.1/Example_Continuous.imzML"p <- parseImzML(path, ibd=TRUE)
p## ImzML: /tmp/RtmpDRqzOc/Rinst2af5e73b561a25/CardinalIO/extdata/Example_Continuous_imzML1.1.1/Example_Continuous.imzML
##
## $fileDescription(3): fileContent sourceFileList contact
## $sampleList(1): sample1
## $scanSettingsList(1): scansettings1
## $softwareList(2): Xcalibur TMC
## $instrumentConfigurationList(1): LTQFTUltra0
## $dataProcessingList(2): XcaliburProcessing TMCConversion
## $run(1): spectrumList
## $ibd(3): uuid mz intensityBy default, only the “.imzML” metadata is parsed. Using ibd=TRUE will also attach the mass spectra (without loading them into memory).
The resulting ImzML object is like a list, and can be traversed in the same way using the standard $, [ and [[ operators.
4.1 Experimental metadata
The experimental metadata is stored in a recursive list structure that closely resembles the XML hierarchy.
4.1.1 File description
The fileDescription element contains basic information about the file’s contents and provenance.
p$fileDescription## $fileContent
## Params list of length 5
##
## MS:1000579 - MS1 spectrum
## MS:1000128 - profile spectrum
## IMS:1000080 - universally unique identifier = 554a27fa79d2...
## IMS:1000091 - ibd SHA-1 = a5be532d2599...
## IMS:1000030 - continuous
##
## $sourceFileList
## $sourceFileList$sf1
## Params list of length 3
## id location name
## sf1 C:\\Users\\Tho... Example.raw
##
## MS:1000563 - Thermo RAW format
## MS:1000768 - Thermo nativeID format
## MS:1000569 - SHA-1 = 7623BE263B25...
##
##
## $contact
## Params list of length 4
##
## MS:1000586 - contact name = Thorsten Sch...
## MS:1000590 - contact affiliation = Institut für...
## MS:1000587 - contact address = Schubertstra...
## MS:1000589 - contact email = thorsten.sch...For example, the cvParam tag below indicates that this imzML file has the “continuous” storage type.
p$fileDescription$fileContent[["IMS:1000030"]]## cv id name
## "IMS" "IMS:1000030" "continuous"4.1.2 Scan settings
If available, the scanSettingsList element contains a list of scan settings that should include information about the image rastering.
p$scanSettingsList## $scansettings1
## Params list of length 10
## id
## scansettings...
##
## IMS:1000401 - top down
## IMS:1000413 - flyback
## IMS:1000480 - horizontal line scan
## IMS:1000491 - linescan left right
## IMS:1000042 - max count of pixels x = 3
## IMS:1000043 - max count of pixels y = 3
## IMS:1000044 - max dimension x = 300 micromet...
## IMS:1000045 - max dimension y = 300 micromet...
## IMS:1000046 - pixel size (x) = 100.0 microm...
## IMS:1000047 - pixel size y = 100.0 microm...The “top down”, “flyback”, “horizontal line scan”, and “linescan left right” terms describe the raster pattern for how the spectra were acquired.
4.1.3 Software
The softwareList element contains information about any software that have been used with the data, including both software to control the acquisition of spectra and software to perform data processing.
p$softwareList## $Xcalibur
## Params list of length 1
## id version
## Xcalibur 2.2
##
## MS:1000532 - Xcalibur
##
## $TMC
## Params list of length 1
## id version
## TMC 1.1 beta
##
## MS:1000799 - custom unreleased software tool4.1.4 Instrument configuration
The instrumentConfigurationList element contains information about the instrument(s) used to acquire the data.
p$instrumentConfigurationList## $LTQFTUltra0
## Params list of length 4
## id
## LTQFTUltra0
##
## MS:1000557 - LTQ FT Ultra
## MS:1000529 - instrument serial number = none
## componentList(3) - ...
## softwareRef - XcaliburEach instrument configuration should include a component list that describes the ion source, mass analyzer, and detector type used.
p$instrumentConfigurationList$LTQFTUltra0$componentList## $source
## Params list of length 11
## order
## 1
##
## MS:1000073 - electrospray ionization
## MS:1000485 - nanospray inlet
## MS:1000844 - focus diameter x = 10.0
## MS:1000845 - focus diameter y = 10.0
## MS:1000846 - pulse energy = 10.0
## MS:1000847 - pulse duration = 10.0
## MS:1000848 - attenuation = 50.0
## MS:1000850 - gas laser
## MS:1000836 - dried droplet MALDI matrix preparation
## MS:1000835 - matrix solution concentration = 10.0
## MS:1000834 - matrix solution = DHB
##
## $analyzer
## Params list of length 2
## order
## 2
##
## MS:1000264 - ion trap
## MS:1000014 - accuracy = 0.0 m/z
##
## $detector
## Params list of length 2
## order
## 3
##
## MS:1000253 - electron multiplier
## MS:1000120 - transient recorder4.1.5 Data processing
The dataProcessingList element contains information about any data processing performed and a reference to the software used to do it.
p$dataProcessingList## $XcaliburProcessing
## $XcaliburProcessing$Xcalibur
## Params list of length 1
## softwareRef order
## Xcalibur 1
##
## MS:1000594 - low intensity data point removal
##
##
## $TMCConversion
## $TMCConversion$TMC
## Params list of length 1
## softwareRef order
## TMC 2
##
## MS:1000544 - Conversion to mzML4.2 Spectrum metadata
The spectrum metadata is the largest part of the imzML file, and therefore is not fully parsed. Many tags in this section are either repeated or unnecessary (and can be safely disregarded) or can be inferred from other tags.
Unlike the experimental metadata, the spectrum metadata are stored as data frames, with a row for each spectrum, rather than in a recursive structure like the original XML.
All data frames are stored in the spectrumList element inside the run element.
Specifically, data frames for positions, mzArrays, and intensityArrays are returned.
Note that no type coercion is performed for the parsed values (they are still strings), so numeric values must be coerced by the user.
4.2.1 Positions
p$run$spectrumList$positions## position x position y position z
## Scan=1 1 1 <NA>
## Scan=2 2 1 <NA>
## Scan=3 3 1 <NA>
## Scan=4 1 2 <NA>
## Scan=5 2 2 <NA>
## Scan=6 3 2 <NA>
## Scan=7 1 3 <NA>
## Scan=8 2 3 <NA>
## Scan=9 3 3 <NA>The positions element gives the pixel x/y-coordinates for each spectrum. The z-coordinates are also available, but rarely used.
4.2.2 m/z metadata
p$run$spectrumList$mzArrays## external offset external array length external encoded length
## Scan=1 16 8399 33596
## Scan=2 16 8399 33596
## Scan=3 16 8399 33596
## Scan=4 16 8399 33596
## Scan=5 16 8399 33596
## Scan=6 16 8399 33596
## Scan=7 16 8399 33596
## Scan=8 16 8399 33596
## Scan=9 16 8399 33596
## binary data type
## Scan=1 32-bit float
## Scan=2 32-bit float
## Scan=3 32-bit float
## Scan=4 32-bit float
## Scan=5 32-bit float
## Scan=6 32-bit float
## Scan=7 32-bit float
## Scan=8 32-bit float
## Scan=9 32-bit floatThe mzArrays element gives information about the locations and storage format of the m/z arrays in the “.ibd” binary data file.
Note that for a “continuous” imzML file (like the one here), each of the rows actually points to the same m/z array. For a “processed” imzML file, each row would point to a different m/z array.
4.2.3 Intensity metadata
p$run$spectrumList$intensityArrays## external offset external array length external encoded length
## Scan=1 33612 8399 33596
## Scan=2 67208 8399 33596
## Scan=3 100804 8399 33596
## Scan=4 134400 8399 33596
## Scan=5 167996 8399 33596
## Scan=6 201592 8399 33596
## Scan=7 235188 8399 33596
## Scan=8 268784 8399 33596
## Scan=9 302380 8399 33596
## binary data type
## Scan=1 32-bit float
## Scan=2 32-bit float
## Scan=3 32-bit float
## Scan=4 32-bit float
## Scan=5 32-bit float
## Scan=6 32-bit float
## Scan=7 32-bit float
## Scan=8 32-bit float
## Scan=9 32-bit floatThe intensityArrays element gives information about the locations and storage format of the intensity arrays in the “.ibd” binary data file.
Note that for a “continuous” imzML file (like the one here), each of the binary data arrays has the same length. For a “processed” imzML file, each spectrum (and therefore the corresponding binary data arrays) could have a different length.
4.3 Mass spectra
If the option ibd=TRUE was used when parsing the imzML file, then the mass spectra data is attached (without loading the data into memory).
p$ibd$mz## <9 length> matter_list :: out-of-memory list
## [1] [2] [3] [4] [5] [6] ...
## $Scan=1 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=2 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=3 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=4 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=5 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=6 100.0833 100.1667 100.2500 100.3333 100.4167 100.5000 ...
## ...
## (6.58 KB real | 302.36 KB virtual)p$ibd$intensity## <9 length> matter_list :: out-of-memory list
## [1] [2] [3] [4] [5] [6] ...
## $Scan=1 0 0 0 0 0 0 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=2 0 0 0 0 0 0 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=3 0 0 0 0 0 0 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=4 0 0 0 0 0 0 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=5 0 0 0 0 0 0 ...
## [1] [2] [3] [4] [5] [6] ...
## $Scan=6 0 0 0 0 0 0 ...
## ...
## (6.58 KB real | 302.36 KB virtual)These out-of-memory lists can be subset like normal lists. They can alternatively be pulled fully into memory using as.list().
mz1 <- p$ibd$mz[[1L]]
int1 <- p$ibd$intensity[[1L]]
plot(mz1, int1, type="l", xlab="m/z", ylab="Intensity")
5 Tracking experimental metadata
The ImzML object should not generally be modified directly.
Instead, the ImzMeta class provides a simplified interface to the tags required for creating a valid imzML file.
5.1 The ImzMeta class
A new ImzMeta instance can be created with ImzMeta():
e <- ImzMeta()
e## ImzMeta: Mass spectrometry imaging experimental metadata
##
## $spectrumType(0):
## $spectrumRepresentation(0):
## $contactName(0):
## $contactAffiliation(0):
## $contactEmail(0):
## $instrumentModel(0):
## $ionSource(0):
## $analyzer(0):
## $detectorType(0):
## $dataProcessing(0):
## $lineScanSequence(0):
## $scanPattern(0):
## $scanType(0):
## $lineScanDirection(0):
## $pixelSize(0):The tags can be assigned via the standard $<- and [[<- operators.
e$spectrumType <- "MS1 spectrum"
e$spectrumRepresentation <- "profile"
e## ImzMeta: Mass spectrometry imaging experimental metadata
##
## $spectrumType(1): MS1 spectrum
## $spectrumRepresentation(1): profile spectrum
## $contactName(0):
## $contactAffiliation(0):
## $contactEmail(0):
## $instrumentModel(0):
## $ionSource(0):
## $analyzer(0):
## $detectorType(0):
## $dataProcessing(0):
## $lineScanSequence(0):
## $scanPattern(0):
## $scanType(0):
## $lineScanDirection(0):
## $pixelSize(0):Note that the "profile" value was automatically expanded to "profile spectrum". Assigning to an ImzMeta object will attempt to match your input the correct controlled vocabulary name, where appropriate.
Trying to assign a value that can’t be unambiguously matched to a valid controlled vocabulary name will yield an error message listing the allowed values.
e$spectrumType <- "spectrum"## Error in validObject(x): invalid class "ImzMeta" object: spectrumType must be one of :'spectrum type', 'mass spectrum', 'PDA spectrum', 'electromagnetic radiation spectrum', 'emission spectrum', 'absorption spectrum', 'calibration spectrum', 'charge inversion mass spectrum', 'constant neutral gain spectrum', 'constant neutral loss spectrum', 'e/2 mass spectrum', 'precursor ion spectrum', 'product ion spectrum', 'MS1 spectrum', 'MSn spectrum', 'CRM spectrum', 'SIM spectrum', 'SRM spectrum', 'enhanced multiply charged spectrum', 'time-delayed fragmentation spectrum'At a bare minimum, spectrumType and spectrumRepresentation must be present to create a valid imzML file (in combination with the mass spectra data and their raster positions). Other fields should be provided, but an imzML file can still be written without them.
5.2 Conversion between ImzML and ImzMeta
Conversion is supported between ImzML and ImzMeta objects.
Converting from ImzMeta to ImzML will keep all ImzMeta metadata. Sensible defaults will be assigned to required-but-missing elements.
p2 <- as(e, "ImzML")
p2## ImzML:
##
## $fileDescription(1): fileContent
## $scanSettingsList(0):
## $softwareList(1): CardinalIO
## $instrumentConfigurationList(1): IC1
## $dataProcessingList(1): CardinalProcessing
## $run(0):p2$fileDescription## $fileContent
## Params list of length 2
##
## MS:1000579 - MS1 spectrum
## MS:1000128 - profile spectrumConverting from ImzML to ImzMeta will lose any metadata that cannot be stored in the simplified ImzMeta object.
e2 <- as(p, "ImzMeta")
e2## ImzMeta: Mass spectrometry imaging experimental metadata
##
## $spectrumType(1): MS1 spectrum
## $spectrumRepresentation(1): profile spectrum
## $contactName(1): Thorsten Schramm
## $contactAffiliation(1): Institut für Anorganische und Analytische Chemie
## $contactEmail(1): [email protected]
## $instrumentModel(1): LTQ FT Ultra
## $ionSource(1): electrospray ionization
## $analyzer(1): ion trap
## $detectorType(1): electron multiplier
## $dataProcessing(0):
## $lineScanSequence(1): top down
## $scanPattern(1): flyback
## $scanType(1): horizontal line scan
## $lineScanDirection(1): linescan left right
## $pixelSize(1): 100.0Support for additional tags may be added to ImzMeta in the future, but some metadata loss is unavoidable due to its simplified format.
As ImzMeta is most useful when constructing metadata from scratch, this should not pose a problem in practice.
5.3 Minimum reporting guidelines
Please note that ImzMeta does not meet minimum reporting guidelines for MS imaging experiments. Its primary purpose is to facilitate an easy interface for editing the required tags to create a valid imzML file.
For example, it does not currently support metadata for samples or sample preparation, as the sampleList tag is not strictly required by the imzML standard. Adding support for sample metadata would require additional ontologies that are currently outside of the scope of this package.
6 Writing imzML files
Writing imzML files is performed with writeImzML(). This is a generic function, so methods can be written to support new classes in other packages. CardinalIO provides methods for ImzML and ImzMeta.
6.1 Writing a file from ImzML metadata
In the simplest case, we can write a parsed imzML file back out.
p## ImzML: /tmp/RtmpDRqzOc/Rinst2af5e73b561a25/CardinalIO/extdata/Example_Continuous_imzML1.1.1/Example_Continuous.imzML
##
## $fileDescription(3): fileContent sourceFileList contact
## $sampleList(1): sample1
## $scanSettingsList(1): scansettings1
## $softwareList(2): Xcalibur TMC
## $instrumentConfigurationList(1): LTQFTUltra0
## $dataProcessingList(2): XcaliburProcessing TMCConversion
## $run(1): spectrumList
## $ibd(3): uuid mz intensitypath2 <- tempfile(fileext=".imzML")
writeImzML(p, file=path2)## [1] TRUE
## attr(,"outpath")
## [1] "/tmp/RtmpfrfO2T/file2affa7c1b2e1b.imzML"In this case, only the “.imzML” file was written and not the “.ibd”, because we did not provide new mass spectra data, which will be demonstrated below.
6.2 Writing a file from ImzMeta metadata
Below, we demonstrate how to write a MS imaging dataset from scratch.
First, we create some simple simulated mass spectra.
set.seed(2023)
nx <- 3
ny <- 3
nmz <- 500
mz <- seq(500, 510, length.out=nmz)
intensity <- replicate(nx * ny, rlnorm(nmz))
positions <- expand.grid(x=seq_len(nx), y=seq_len(ny))
plot(mz, intensity[,1], type="l", xlab="m/z", ylab="Intensity")
Next, we create some metadata.
meta <- ImzMeta(spectrumType="MS1 spectrum",
spectrumRepresentation="profile",
instrumentModel="LTQ FT Ultra",
ionSource="electrospray ionization",
analyzer="ion trap",
detectorType="electron multiplier")
meta## ImzMeta: Mass spectrometry imaging experimental metadata
##
## $spectrumType(1): MS1 spectrum
## $spectrumRepresentation(1): profile spectrum
## $contactName(0):
## $contactAffiliation(0):
## $contactEmail(0):
## $instrumentModel(1): LTQ FT Ultra
## $ionSource(1): electrospray ionization
## $analyzer(1): ion trap
## $detectorType(1): electron multiplier
## $dataProcessing(0):
## $lineScanSequence(0):
## $scanPattern(0):
## $scanType(0):
## $lineScanDirection(0):
## $pixelSize(0):Now, we can write the file using writeImzmL().
path3 <- tempfile(fileext=".imzML")
writeImzML(meta, file=path3, positions=positions, mz=mz, intensity=intensity)## [1] TRUE
## attr(,"outpath")
## [1] "/tmp/RtmpfrfO2T/file2affa73a4d403c.imzML"
## [2] "/tmp/RtmpfrfO2T/file2affa73a4d403c.ibd"7 Session information
sessionInfo()## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] CardinalIO_1.2.1 ontologyIndex_2.12 matter_2.6.1
## [4] Matrix_1.7-0 BiocParallel_1.38.0 BiocStyle_2.32.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.2 knitr_1.46 magick_2.8.3
## [4] rlang_1.1.3 xfun_0.43 ProtGenerics_1.36.0
## [7] highr_0.10 DBI_1.2.2 jsonlite_1.8.8
## [10] S4Vectors_0.42.0 htmltools_0.5.8.1 tinytex_0.51
## [13] sass_0.4.9 stats4_4.4.0 rmarkdown_2.26
## [16] grid_4.4.0 evaluate_0.23 jquerylib_0.1.4
## [19] fastmap_1.1.1 yaml_2.3.8 lifecycle_1.0.4
## [22] bookdown_0.39 BiocManager_1.30.23 compiler_4.4.0
## [25] codetools_0.2-20 irlba_2.3.5.1 Rcpp_1.0.12
## [28] lattice_0.22-6 digest_0.6.35 R6_2.5.1
## [31] parallel_4.4.0 magrittr_2.0.3 bslib_0.7.0
## [34] tools_4.4.0 biglm_0.9-2.1 BiocGenerics_0.50.0
## [37] cachem_1.0.8