Posted by
Cammer, Michael-2 on
URL: http://imagej.273.s1.nabble.com/BioFormats-and-Zen-Black-Blue-cannot-handle-large-images-generated-with-Zen-Blue-tp5021136.html
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:
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http://nyulmc.org/micros http://microscopynotes.com/Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567
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