Hi everyone,<br><br>Below is a recent discussion on fiji-users about exporting very large TIFF files (i.e., BigTIFF needed).<br><br>I looked at the source code for TiffWriter and think it would be doable to automatically turn on the isBigTiff flag if the total size of all planes to be written exceeds the 4GB threshold. This check would happen once, just prior to calling tiffSaver.writeHeader(), so the correct header type gets written. The only tricky bit is at the edge case where the IFD metadata might push the file over the limit. One (hacky) way around this issue would be to switch to BigTIFF when the pixel data is even close: say, over 3.5GB.<br>
<br>Do you agree this would be a good idea? If so, can we file a ticket for it?<br><br>Thanks,<br>Curtis<br><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Curtis Rueden</b> <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a>></span><br>
Date: 2012/4/10<br>Subject: Re: [fiji-users] Large tiff files<br>To: Sébastien Tosi <<a href="mailto:sebastien.tosi@gmail.com">sebastien.tosi@gmail.com</a>><br>Cc: Fiji-users <<a href="mailto:fiji-users@googlegroups.com">fiji-users@googlegroups.com</a>><br>
<br><br>Hi Sébastien,<div class="im"><br><br><br><blockquote style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">Thank you Curtis, I tried the Bio-formats exporter but it failed with an
error message telling that the BigTiff flag should be enabled. Do you
know how to configure it? Anyway I decided to export the stack as a
sequence of images to import it in the other program.<span></span><br><span></span></blockquote><span><font color="#888888">
</font></span><br></div>Hmm, sorry about that. I thought the Exporter was smart enough to switch to BigTIFF as needed. I will talk to the other Bio-Formats developers about making it smarter (should be easy).<br><br>Regards,<br>
Curtis<div class="HOEnZb"><div class="h5"><br><br><br><div class="gmail_quote">2012/4/10 Sébastien Tosi <span dir="ltr"><<a href="mailto:sebastien.tosi@gmail.com" target="_blank">sebastien.tosi@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you Curtis, I tried the Bio-formats exporter but it failed with an error message telling that the BigTiff flag should be enabled. Do you know how to configure it? Anyway I decided to export the stack as a sequence of images to import it in the other program.<span><font color="#888888"><br>
<br>Sébastien</font></span><div><div><br><br><div class="gmail_quote">On 5 April 2012 18:36, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Sébastien,<br><br><blockquote style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">It seems the limit is around 4.2 GB, all<br>
file above this limit suffering the problem.<br></blockquote><br>TIFFs have an inherent 32-bit limit (~4GB as you note). Try using the Bio-Formats Exporter to write out your TIFFs, which will use the 64-bit BigTIFF format as needed when exporting.<br>
<br>Regards,<br>Curtis<br><br><br><div class="gmail_quote">2012/4/5 Sébastien Tosi <span dir="ltr"><<a href="mailto:sebastien.tosi@gmail.com" target="_blank">sebastien.tosi@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
Large z-stack are saved improperly as tiff files by the built-in<br>
ImageJ tiff filter. The stacks can be read by ImageJ but any other<br>
software fail to open them... inspecting the header of the files (in<br>
Matlab) it shows that only a single plane is present in the file. I am<br>
working with single frame 8-bit series with around 500 z planes and<br>
3000x3000 pixels per plane. It seems the limit is around 4.2 GB, all<br>
file above this limit suffering the problem.<br>
<span><font color="#888888"><br>
Sébastien<br>
<br>
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