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Reading OME-Zarr (OME-NGFF) #34
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Hi Ludwig, many thanks for reaching out! Indeed, it seems that adding zarrreader java library to the classpath used by RBioFormats is sufficient to enable reading of OME-Zarr file format, see below. The example queries only for image metadata because when trying to read pixel data I've run into an issue described in ome/ZarrReader#45. library(RBioFormats)
library(rJava)
zarrfile = "/Users/oles/Downloads/v0.4/yx.ome.zarr/.zattrs"
zarrreader = "/Users/oles/Projects/ZarrReader/target/OMEZarrReader-0.3.1-SNAPSHOT-jar-with-dependencies.jar"
.jaddClassPath(zarrreader, class.loader = .jclassLoader(package="RBioFormats"))
read.metadata(zarrfile)
#> ImageMetadata list of length 3
#>
#> series res sizeX sizeY sizeC sizeZ sizeT total
#> 1 1 1024 930 1 1 1 1
#> 1 2 512 465 1 1 1 1
#> 1 3 256 232 1 1 1 1
#>
#> globalMetadata:List of 4
#> $ Axis type:0:0: chr "space"
#> $ Axis name:0:1: chr "x"
#> $ Axis name:0:0: chr "y"
#> $ Axis type:0:1: chr "space" Created on 2023-01-10 with reprex v2.0.2 AFAIU obtaining the ZarrReader jar file currently requires building it from sources. It would certainly ease things up quite a bit if ZarrReader was available already packaged. @sbesson any plans regarding this? Cheers, |
Hi @aoles! You can see how the jar is pulled into OMERO from Maven here: https://github.com/ome/openmicroscopy/blob/develop/ivy.xml#L21 |
A discussion in the Bioconductor slack channel was wondering whether RBioFormats could already be used to read OME-Zarr format. It seems that with the additional https://github.com/ome/zarrreader jar, RBioFormats would be able to read OME-Zarr (i.e. OME-NGFFs)?
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