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Hi Maxime,
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<div class="">We have been able to further debug the first issue to identify how the problem occurs but we do not yet have a fix in place for it.</div>
<div class="">You can follow the progress of that issue on the Trello card here: <a href="https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count" class="">https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count</a></div>
<div class=""><br class="">
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<div class="">With regards the second issue I have still been unable to reproduce it. If I open the 2 converted files you had originally attached (one converted with bfconvert, the other with FIJI) both open and display the same when using the latest FIJI install. </div>
<div class="">When you converted the TIFF image using FIJI, and when you read the image back, was that using the Bio-Formats exporter and importer? </div>
<div class=""><br class="">
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 1 Sep 2017, at 18:59, Maxime Woringer <<a href="mailto:maxime.woringer@berkeley.edu" class="">maxime.woringer@berkeley.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi
David,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Do
you have any update about the two bugs mentioned earlier? Were you</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">able
to reproduce the second bug mentioned in my previous email?</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thanks
a lot,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Maxime</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">David
Gault (Staff) <</span><a href="mailto:d.gault@dundee.ac.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">d.gault@dundee.ac.uk</a><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">>
writes:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Hi Maxime,<br class="">
<br class="">
Thank for reporting this issue and for providing sample files to test with.<br class="">
I can certainly reproduce the first the issue using the sample files provided and this does indeed look to be a bug.<br class="">
For the second issue I was unable to reproduce using bfconvert from the latest Bio-Formats release, and in theory the conversion should be the same as the FIJI result.<br class="">
Would you be able to run bfconvert -version to confirm that bftools is using the latest jars?<br class="">
<br class="">
I have created a Trello card on the Bio-Formats inbox for further investigation into these issues:<span class="Apple-converted-space"> </span><a href="https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count" class="">https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count</a><br class="">
<br class="">
With Thanks,<br class="">
David Gault<br class="">
<br class="">
On 14 Aug 2017, at 04:01, Maxime Woringer <<a href="mailto:maxime.woringer@berkeley.edu" class="">maxime.woringer@berkeley.edu</a><<a href="mailto:maxime.woringer@berkeley.edu" class="">mailto:maxime.woringer@berkeley.edu</a>>> wrote:<br class="">
<br class="">
Dear Bio-Formats users/developers,<br class="">
<br class="">
I am trying to convert ND2 files (acquired with NIkon NIS elements) to<br class="">
TIFF files, ideally in an automated fashion, but I am encountering<br class="">
issues that seem to me like bugs (but I'd be happy to be proven wrong).<br class="">
<br class="">
1. Some single images appear corrupted when I try to convert them to<br class="">
TIFF. Below is an example. The two files (BF007 and BF008) were created<br class="">
on the same machine, same software, at a 30' interval. I am not aware of<br class="">
any differing setting except the ROI size.<br class="">
- BF008.nd2 opens properly in Fiji and converts properly using bfconvert<br class="">
(laters version). I am attaching the .nd2 file, the resulting TIFF file,<br class="">
and the convert log (.txt files) and a screenshot of how Fiji opens it.<br class="">
- BF008.nd2 opens corrupted in Fiji, and the same result happens using<br class="">
bfconvert. It seems that BF thinks it is a 3-channel image (it is not).<br class="">
<BF007.nd2><BF007.txt><BF007-bf.tiff><BF007-Capture du 2017-08-13 18-50-59.png><BF008.nd2><BF008.txt><BF008-bf.tiff><BF008-Capture du 2017-08-13 18-50-53.png><br class="">
2. Now moving to ND2 TIFF series (one channel, multiple timepoints),<br class="">
they open fine in Fiji using BioFormats, however, if I use the following<br class="">
command:<br class="">
<br class="">
bftools/bfconvert in.nd2 out.tiff<br class="">
<br class="">
The resulting TIFF file opens totally corrupted in Fiji/ImageJ (note<br class="">
that the first frame is fine).<br class="">
<br class="">
Below are an example source file (nd2), the conversion result using<br class="">
bfconvert, and the conversion result using Fiji. I am attaching the<br class="">
bfconvert log (convert.log)<br class="">
<convert.log>- Source ND2 file: <a href="https://cloud.biologie.ens.fr/index.php/s/H7OPHzLvJ3MPUkd" class="">
https://cloud.biologie.ens.fr/index.php/s/H7OPHzLvJ3MPUkd</a><br class="">
- Corrupted TIFF generated by bfconvert: <a href="https://cloud.biologie.ens.fr/index.php/s/FFOIjHUg6Dl7B1I" class="">
https://cloud.biologie.ens.fr/index.php/s/FFOIjHUg6Dl7B1I</a><br class="">
- Correct TIFF generated by Fiji: <a href="https://cloud.biologie.ens.fr/index.php/s/dyl1hZha3pGiP50" class="">
https://cloud.biologie.ens.fr/index.php/s/dyl1hZha3pGiP50</a><br class="">
<br class="">
Finally, I should mention that at least the latter issue happens with<br class="">
files generated with several versions of NIS elements.<br class="">
<br class="">
Am I the only person experiencing those issues? Is there any kind of<br class="">
additional information I should provide?<br class="">
<br class="">
- Version information: bf 5.5.3 and/or Fiji (latest update)<br class="">
- OS: I encounter the issue on Ubuntu 14.04 and Debian Jessie (8.9)<br class="">
- java version: I believe the one used is packaged by BioFormats, but in<br class="">
case, java -version returns<br class="">
Ubuntu machine:<br class="">
java version "1.8.0_144"<br class="">
Java(TM) SE Runtime Environment (build 1.8.0_144-b01)<br class="">
Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)<br class="">
Debian machine:<br class="">
java version "1.7.0_131"<br class="">
OpenJDK Runtime Environment (IcedTea 2.6.9) (7u131-2.6.9-2~deb8u1)<br class="">
OpenJDK 64-Bit Server VM (build 24.131-b00, mixed mode)<br class="">
<br class="">
Thanks a lot!<br class="">
Maxime<br class="">
<br class="">
PS: I tried to upload the files to the QA systemn, but it complains that<br class="">
my version of Flash is not up-to-date. I apologize about that and hope<br class="">
that you will be able to retrieve the files linked/attached.<br class="">
PPS: I have checked the "Common issues to check" page before sending<br class="">
this email, and I believe that none of them apply.<br class="">
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