Opened 7 years ago

Last modified 7 years ago

#62 new enhancement

zvi to jpx

Reported by: boris Owned by: fedorov
Priority: minor Milestone: Future
Component: libbioimage Version:
Keywords: Cc:

Description

Our main issue is converting image stack files from .CZI (Carl Zeiss Images) format to .JPX (3D JPEG2000) format.

In brief, we're getting CZI files from a microscope slide contour (via Zeiss's ZEN software) that are 500-800 GB, and we'd like to acquire three contours at a time (~4h each), rotate and flip them, then save as 1:10 compressed (lossy) JPX files for use by Stereo Investigator software (by MBF Bioscience), all batched overnight.

Would you have any suggestions as to how we can automate file conversion of .CZI to .JPX (or even to .JP2), please?

[Because we haven't been able to directly convert CZI to JPX, we've been exporting from ZEN as TIFFs, rotating/flipping, then saving manually as JPX using MBF's Biolucida Converter (we have as a demo for now). Unfortunately, ZEN has an export limit of 2GB, and TIFFs themselves seem to have a limit of ~4GB, so our large image stacks have to broken into ~8 smaller pieces before export, and then manually "stitched" back together in Stereo Investigator. It's taking about ~15h (incl. ~2h person-time spread over ~8h, and incl. some computing down-time) to do one contour, which is not feasible given the scale of our project (350 contours for each of several experiments).]

UCSF Center for Memory and Aging

Change History (1)

comment:1 Changed 7 years ago by fedorov

  • Component changed from bimread to libbioimage
  • Milestone changed from 1.66 to Future

Hi,

Note ZVI is a different file format from CZI.

Our main issue is converting image stack files from .CZI (Carl Zeiss Images) format to .JPX (3D JPEG2000) format.

In brief, we're getting CZI files from a microscope slide contour (via Zeiss's ZEN

software) >that are 500-800 GB, and we'd like to acquire three contours at a time (~4h each), rotate and >flip them, then save as 1:10 compressed (lossy) JPX files for use by Stereo Investigator >software (by MBF Bioscience), all batched overnight.

Would you have any suggestions as to how we can automate file conversion of .CZI to .JPX (or even to .JP2), please?

libbioimage does not support CZI as of now. In fact it does not support JPEG2000 either. So in order to use libbioimage both of these formats would have to be plugged in. Java-based Bioformats library partially supports CZI files but we didn't have good luck with large files like you are describing they also claim to support JPEG2000 but I have never tested that.

Before I elaborate. We are looking at adding CZI support using a proprietary library into our Web system Bisque though we will probably not add that into libbioimage immediately. That may happen eventually once that proprietary tool is open sourced.

If you are interested in working with us to create open source CZI decoder we could discuss that. Adding JPEG2000 would be rather easy, I already have some older code using libJasper which could be plugged-in rather rapidly although libjasper is now very old and probably libjpeg is a more interesting option to explore.

[Because we haven't been able to directly convert CZI to JPX, we've been exporting from ZEN as TIFFs, rotating/flipping, then saving manually as JPX using MBF's Biolucida Converter (we have as a demo for now). Unfortunately, ZEN has an export limit of 2GB, and TIFFs themselves seem to have a limit of ~4GB, so our large image stacks have to broken into ~8 smaller pieces before export, and then manually "stitched" back together in Stereo Investigator. It's taking about ~15h (incl. ~2h person-time spread over ~8h, and incl. some computing down-time) to do one contour, which is not feasible given the scale of our project (350 contours for each of several experiments).]

Standard TIFF files can only support up to 4GB but BigTIFF and OME-BigTIFF can support very large files, in fact libbioimage works with 26GB 5D OME-BigTIFF files regularly in our workflow. As of now we use Imaris to export tiff planes from a CZI file and then use bioimgconvert to create a 5D OME-BigTIFF. Soon we should be able to import CZI directly into Bisque and export in any supported format (JPEG2000 is not yet supported).

We can discuss in more detail about collaboration regarding adding these formats. My suggestion would be to write to our google groups (bisque-bioimage) since this discussion might be interesting for other users:

https://groups.google.com/forum/#!forum/bisque-bioimage

-dmitry

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