CZIReader in BioFormats does not support reading CZIs compressed using ZSTD

[zeissmicroscopy]

Hi all,

I am not sure if you are aware of the fact that some ZEN version already and very soon all ZEN version will be able to save CZI using the ZSTD compression

https://github.com/facebook/zstd

This new, very fast and efficient compression is already implemented internally in ZEN and in our new libCZIrw (C++, soon on Github) library as well as inside our pylibCZIrw

I gave the latest BioFormats in Fiji I try and got errors, but i think it should be supported since BioFormats 6.8.0.

Here the link to the file: https://www.dropbox.com/s/wcvqr2k1pagtwcm/w96_A1%2BA2_analyzed_ZSTD.czi?dl=0

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 168MB of 24379MB (<1%)

java.lang.NoClassDefFoundError: io/airlift/compress/zstd/ZstdDecompressor
    at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:4100)
    at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:4017)
    at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:4012)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:773)
    at loci.formats.FormatReader.setId(FormatReader.java:1443)
    at loci.formats.ImageReader.setId(ImageReader.java:849)
    at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:472)
    at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:450)
    at io.scif.AbstractParser.parse(AbstractParser.java:244)
    at io.scif.AbstractParser.parse(AbstractParser.java:314)
    at io.scif.AbstractParser.parse(AbstractParser.java:53)
    at io.scif.AbstractReader.setSource(AbstractReader.java:271)
    at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:91)
    at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
    at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
    at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
    at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
    at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:94)
    at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:52)
    at org.scijava.io.DefaultIOService.open(DefaultIOService.java:93)
    at org.scijava.io.DefaultIOService.open(DefaultIOService.java:68)
    at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:549)
    at HandleExtraFileTypes.run(HandleExtraFileTypes.java:97)
    at ij.IJ.runUserPlugIn(IJ.java:241)
    at ij.IJ.runPlugIn(IJ.java:204)
    at ij.IJ.runPlugIn(IJ.java:193)
    at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:518)
    at ij.io.Opener.openUsingHandleExtraFileTypes(Opener.java:372)
    at ij.io.Opener.openImage(Opener.java:359)
    at ij.io.Opener.openImage(Opener.java:243)
    at ij.io.Opener.open(Opener.java:109)
    at ij.io.Opener.openAndAddToRecent(Opener.java:292)
    at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:194)
    at ij.plugin.DragAndDrop.run(DragAndDrop.java:160)
    at java.lang.Thread.run(Thread.java:748)

[zeissmicroscopy]

Ok, I think I am missing a dependency, but for users it is not clear where to get it?

io.airlift.aircompressor ?

[dgault]

Hi @zeissmicroscopy, yes the ZSTD compression should be supported and testing the sample file with the latest release does not show any errors. How are you accessing Bio-Formats, is it through the command line tools, FIJI, or another method? If you are using a download of the Bio-Formats package or command line tools from https://www.openmicroscopy.org/bio-formats/downloads/, then the dependency will be included. For FIJI the aircompressor dependency should come as part of the main install (from Fiji 2.4.0 onwards).

[sebi06]

Hi @dgault ,

after all the ongoing Fiji updates I check again and you are correct. The JAR is there :-). Therefore I think this issue can be closed.

[dgault]

Thanks, glad to hear that everything is sorted