Saving OIB: metadata is lost

[hmbotelho]

When saving this OIB file with RBioFormats the pixel size metadata is lost.

Here's what I did:

library(RBioFormats)
img = read.image("Image0010_01.oib", normalize = FALSE)[,,2]
write.image(img, "Image0010_01.ome.tiff", force = TRUE, pixelType = "uint16")

Doing the equivalent using the bfconvert command line tool preserves the pixel size metadata:

bfconvert Image0010_01.oib Image0010_01.ome.tiff

More info here: https://github.com/hmbotelho/oib_to_tif

[aoles]

Thanks a lot for reporting this! Actually, when converting an OIB file to OME.TIFF pixel size metadata seems to be preserved both by bfconvert and RBioFormats.

library(RBioFormats)
#> Loading required package: rJava
#> BioFormats library version 6.9.1

fname_oib <- "Image0010_01.oib"
oib <- read.image(fname_oib, normalize = FALSE, subset = list(C = 2))

globalMetadata(oib, pattern = "WidthConvertValue|HeightConvertValue|WidthUnit")
#> $`[Reference Image Parameter] WidthUnit`
#> [1] "um"
#> 
#> $`[Reference Image Parameter] HeightConvertValue`
#> [1] "6.214"
#> 
#> $`[Reference Image Parameter] WidthConvertValue`
#> [1] "6.214"

fname_tif <- sub(".oib", ".ome.tif", fname_oib)
write.image(oib, fname_tif, force = TRUE)
tif <- read.image(fname_tif, normalize = FALSE)

globalMetadata(tif, pattern = "WidthConvertValue|HeightConvertValue|WidthUnit")
#> $`[Reference Image Parameter] WidthUnit`
#> [1] "um"
#> 
#> $`[Reference Image Parameter] HeightConvertValue`
#> [1] "6.214"
#> 
#> $`[Reference Image Parameter] WidthConvertValue`
#> [1] "6.214"

^{Created on 2022-05-17 by the reprex package (v2.0.1)}

Nevertheless, there seem to be some problem in handling of resolution-related metadata entries in the case of plain TIFF files, as illustrated by the following example. I will look into this, so stay tuned.

library(RBioFormats)
#> Loading required package: rJava
#> BioFormats library version 6.9.1

fname_oib <- "Image0010_01.oib"
fname_tif <- sub(".oib", ".tif", fname_oib)

oib <- read.image(fname_oib, normalize = FALSE, subset = list(C = 2))
write.image(oib, fname_tif, force = TRUE)
tif <- read.image(fname_tif, normalize = FALSE)

globalMetadata(tif, pattern = "Resolution")
#> $YResolution
#> [1] 0
#> 
#> $ResolutionUnit
#> [1] "Centimeter"
#> 
#> $XResolution
#> [1] 0

system(sprintf("bfconvert -channel 1 -overwrite %s %s", fname_oib, fname_tif))
tif <- read.image(fname_tif, normalize = FALSE)

globalMetadata(tif, pattern = "Resolution")
#> $YResolution
#> [1] 1609.269
#> 
#> $ResolutionUnit
#> [1] "Centimeter"
#> 
#> $XResolution
#> [1] 1609.269

^{Created on 2022-05-17 by the reprex package (v2.0.1)}

[hmbotelho]

Thanks for checking this out and comparing TIF and OME.TIFF

Indeed the resolution metadata is stored by RBioFormats, but in a way which is not accessible to Fiji (which my downstream workflow relies on).

I think I found the source of the issue. It sems to be one OME-XML metadata field, which bftools sets as:
<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="6.214" PhysicalSizeXUnit="µm" PhysicalSizeY="6.214" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SignificantBits="12" SizeC="2" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" TimeIncrement="1.0" TimeIncrementUnit="s" Type="uint16">

and RBioFormats sets as
<Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" SignificantBits="16" SizeC="1" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint16">

Is there a way to edit this metadata field in RBioFormats? I checked the Metadata setting functions but did not know how to use them.

Maybe this approach can also help in dealing with plain TIFF files?