RBioFormats
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aoles
:books: R interface to the Bio-Formats library
Would it be possible to add a function to edit the XML metadata of the OME-TIFF file? Say for instance, I'm only keeping a lower resolution from a pyramid (to...
Specifically the documentation of the `subset` argument, which isn't very clear. I need to look into the source code to figure out what to put for `subset` when reading in...
Hello, I am a bit at a loss. I am developing a package that requires `RBioFormats::read.image()` to lead subsections of images. THus, I need to spin up a java VM...
Hi, I tried to install RBioFormats on R4.3.0: `BiocManager::install("aoles/RBioFormats")` ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/9771460.1.SC1.q/RtmptHlfNa/remotes5b886ec82ce9/aoles-RBioFormats-5ec5fad/DESCRIPTION’ ... OK * preparing ‘RBioFormats’: * checking DESCRIPTION meta-information ... OK...
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...
The package shouldn't depend on an active internet connection, at least not without properly informing users, and definitely should not rely on a single server which today failed and renders...
This should pass `R CMD check --as-cran` and have continuous integration of Windows and Linux with Travis/Appveyor.
Getting this trying to install on: CentOS Linux release 7.7.1908 (Core) R Under development (unstable) (2022-02-17 r81751) -- "Unsuffered Consequences" Any ideas? Thanks, Doug > library(rJava) > .jinit() > .jcall("java/lang/System",...
When saving [this OIB file](https://github.com/hmbotelho/oib_to_tif/raw/main/Image0010_01.oib) 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,...
I'm using RBioFormats v0.0.57 and rJava v0.9-13. After last update of RBioFormats, thanks to add the possibility to load without internet connection. A pair of days ago, I noticed the...
