BioFormats and Zen Black/Blue cannot handle large images generated with Zen Blue

[Cammer, Michael-2]

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]>  http://nyulmc.org/micros  http://microscopynotes.com/
Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567



------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

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[Curtis Rueden]

Hi Michael,

Please consider posting this on the Image.sc Forum (https://forum.image.sc).
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 - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/



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]>
> http://nyulmc.org/micros  http://microscopynotes.com/
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>
>
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Cammer, Michael-2]

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 - https://urldefense.proofpoint.com/v2/url?u=https-3A__loci.wisc.edu_software&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=kt7jUhFhtuhiTnZM1LVa9z1Ku1s--3feceZTJsL9R0o&e=
ImageJ2 lead, Fiji maintainer - https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_User-3ARueden&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=GpZ5A7KhGoUqMYNI_VD38gzENR5NQmekjDZjhC6FVc8&e=
Did you know ImageJ has a forum? https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.imagej.net_&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=Z07S-l_L9h-clsBGH11SNJ9FdIO0w3i4XlpCg9YDnuM&e=



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]>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=pGoMAA77B3gv27IVxlil-GwbtejuhBGs1lhFmU4GQbA&e=  https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=DAtbviz3adCqU54zjBzQTDG9Z32tI7sLY3QIwbEwUm4&e=
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>
>
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
> --
> ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=e60lJccFwCohjTKKg7rDDjX8g0HT59THg5fTUJv8ITs&e=
>

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------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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[Curtis Rueden]

Hi Michael,

> The problem here is that BioFormats will not open a 13 GB CZI file
properly.

The recommended way to report Bio-Formats bugs is the ome-users mailing
list.


https://docs.openmicroscopy.org/bio-formats/5.9.1/about/bug-reporting.html#sending-a-bug-report

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Aug 28, 2018 at 4:32 PM Cammer, Michael <
[hidden email]> wrote:

> 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 -
> https://urldefense.proofpoint.com/v2/url?u=https-3A__loci.wisc.edu_software&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=kt7jUhFhtuhiTnZM1LVa9z1Ku1s--3feceZTJsL9R0o&e=
> ImageJ2
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__loci.wisc.edu_software&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=kt7jUhFhtuhiTnZM1LVa9z1Ku1s--3feceZTJsL9R0o&e=ImageJ2>
> lead, Fiji maintainer -
> https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_User-3ARueden&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=GpZ5A7KhGoUqMYNI_VD38gzENR5NQmekjDZjhC6FVc8&e=
> Did you know ImageJ has a forum?
> https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.imagej.net_&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=Z07S-l_L9h-clsBGH11SNJ9FdIO0w3i4XlpCg9YDnuM&e=
>
>
>
> 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]>
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=pGoMAA77B3gv27IVxlil-GwbtejuhBGs1lhFmU4GQbA&e=
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=DAtbviz3adCqU54zjBzQTDG9Z32tI7sLY3QIwbEwUm4&e=
> > Voice direct only, no text or messages:  1-914-309-3270 and
> 1-646-501-0567
> >
> >
> >
> > ------------------------------------------------------------
> > This email message, including any attachments, is for the sole use of the
> > intended recipient(s) and may contain information that is proprietary,
> > confidential, and exempt from disclosure under applicable law. Any
> > unauthorized review, use, disclosure, or distribution is prohibited. If
> you
> > have received this email in error please notify the sender by return
> email
> > and delete the original message. Please note, the recipient should check
> > this email and any attachments for the presence of viruses. The
> > organization accepts no liability for any damage caused by any virus
> > transmitted by this email.
> > =================================
> >
> > --
> > ImageJ mailing list:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=4CA-Ex9FRT5elTO7T6Dezw_PPfeKf-WamRFIRselam0&s=e60lJccFwCohjTKKg7rDDjX8g0HT59THg5fTUJv8ITs&e=
> >
>
> --
> ImageJ mailing list:
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>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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