http://imagej.273.s1.nabble.com/BioFormats-and-Zen-Black-Blue-cannot-handle-large-images-generated-with-Zen-Blue-tp5021136p5021137.html
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
export routine. Etc.
> 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
>
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