http://imagej.273.s1.nabble.com/BioFormats-and-Zen-Black-Blue-cannot-handle-large-images-generated-with-Zen-Blue-tp5021136p5021139.html
> Zen won't export it as Big TIFF or any other flavor of file.
>
> The problem here is that BioFormats will not open a 13 GB CZI file
> properly. We would very much appreciate having this addressed.
>
> Cheers-
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> 10016
>
[hidden email] http://nyulmc.org/micros>
http://microscopynotes.com/> Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Tuesday, August 28, 2018 5:27 PM
> To:
[hidden email]
> Subject: Re: BioFormats and Zen Black/Blue cannot handle large images
> generated with Zen Blue
>
> Hi Michael,
>
> Please consider posting this on the Image.sc Forum (
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__forum.image.sc&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=vfqSyP34dHEmKth6kalTRBhBjF2h5ny7eh9iABnhits&e=> ).
> If you did, we would be able to invite/mention the relevant OME, Zeiss and
> ImageJ developers, so this can be more easily discussed in one common
> place.
>
> On the Bio-Formats/ImageJ side, please note that TIFF is limited to 4GB in
> size. A 13GB TIFF is either a BigTIFF, an ImageJ1-flavored TIFF, or
> possibly some Zeiss variant TIFF. If it is a well-formed BigTIFF,
> Bio-Formats is supposed to handle it, and failure to do so is a bug. If it
> is not well-formed, that is probably a bug in the Zeiss software's BigTIFF
> export routine. Etc.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
>
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>
>
> On Tue, Aug 28, 2018 at 4:19 PM Cammer, Michael <
>
[hidden email]> wrote:
>
> > We have a problem that we have images that we need as TIF but neither Zen
> > Blue, where they are generated, nor ImageJ with BioFormats can open them.
> >
> > The images are 16 bits 3 channels tiles taken with a CCD camera with Zen
> > Blue. The files were stitched with "Fuse Tiles" checked. The goal is to
> > have each channel as one big image.
> >
> > When the files are up to 3 GB or so, BioFormats opens them fine (and
> we're
> > really happy with this). But when they are larger (we haven't tested the
> > size threshold), BioFormats does not open them.
> >
> > We tried a work around by exporting from Zen Blue to TIF, but this does
> > not work. None of the TIF options, (Big Tiff, OME TIFF, etc) work. They
> > export folders of tif files of varying sizes or convert to RGB or simply
> > gives a message that the files are too big. We also tried opening the
> > files in Zen Black and restitching them, but this fails too. So Zen
> takes
> > the pictures and lets us work with them in Zen, but there is no way to
> get
> > the images out for use with any other software either using their native
> > formats LSM and CZI or via TIF. (Although we would prefer to use
> > BioFormats, it would also be great for Zeiss to include an export
> function
> > that works. We complained about this with past versions of Zen and the
> > recent upgrade doesn't handle this any better.)
> >
> > We would very much appreciate help with this and could upload an example
> > CZI image (approx 13 GB) somewhere if this would help.
> >
> > We would very much like to have a SOP for people tiling multichannels to
> > work with them in ImageJ and extract each stitched channel as one big
> image.
> >
> > Thank you!
> >
> > Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> > NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> > 10016
> >
[hidden email]<mailto:
[hidden email]>
> >
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