Use the python package tifffile to get the the XML metadata of a .tif file. The R package {xml2} is then used to work with it to retrieve specific nodes in the xml data and extract data.
Usage
tif_metadata(
path,
node = NULL,
page = NULL,
type = c("attribute", "text", "double", "integer"),
output = c("data.frame", "xml", "list", "structure")
)
ometif_metadata(
path,
node = NULL,
page = NULL,
type = c("attribute", "text", "double", "integer"),
output = c("data.frame", "xml", "list", "structure")
)Arguments
- path
character. filepath to tif image
- node
character vector. Specific xml node to get. More terms can be added to get a node from a specific hierarchy.
- page
numeric. Specific page to get metadata from. Currently only used for
.qptiff.- type
character. Type of data to extract. Only affects
output = data.frame(Matches to one of "attribute", "text", "double", "integer").output = "structure"can help with figuring out which is most appropriate.- output
character. One of "data.frame" to return a data.frame of the attributes information of the xml node, "xmL" for an {xml2} representation of the node, "list" for an R native list (note that many items in the list may have overlapping names that make indexing difficult), or "structure" to invisibly return NULL, but print the structure of the XML document or node.
See also
Other tif utility functions:
to_simple_tif()
Examples
if (FALSE) {
# check structure of metadata
tif_metadata("path/to/ometif", output = "structure")
# xenium morphology ometif - find channels/biomarkers
tif_metadata("path/to/ometif", node = "Channel")
# phenocycler qptiff - find channels/biomarkers
tif_metadata("path/to/qptiff",
page = NULL,
node = "Biomarker",
type = "text"
)
}