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Hi Maxime,
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<div class="">Thank for reporting this issue and for providing sample files to test with.</div>
<div class="">I can certainly reproduce the first the issue using the sample files provided and this does indeed look to be a bug.</div>
<div 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. </div>
<div class="">Would you be able to run bfconvert -version to confirm that bftools is using the latest jars?</div>
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<div class="">I have created a Trello card on the Bio-Formats inbox for further investigation into these issues: <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>
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<div class="">With Thanks,</div>
<div class="">David Gault<br class="">
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<blockquote type="cite" class="">
<div class="">On 14 Aug 2017, at 04:01, Maxime Woringer <<a href="mailto:maxime.woringer@berkeley.edu" class="">maxime.woringer@berkeley.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div 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="">
<span id="cid:18F23827-4358-4060-B329-54A9DF4C0C7A@Home"><BF007.nd2></span><span id="cid:BEF6170E-5F0C-4D44-B46B-2C2C167E6114@Home"><BF007.txt></span><span id="cid:5CF31E03-B50C-4D5D-B83A-D4456CB05DEE@Home"><BF007-bf.tiff></span><span id="cid:E67BD19A-3892-462B-9BD2-474308AD19F2@Home"><BF007-Capture
du 2017-08-13 18-50-59.png></span><span id="cid:91138C16-B068-487A-A701-E505922BCDC5@Home"><BF008.nd2></span><span id="cid:942ABF1E-2CD4-41FC-B06B-5F1215D11455@Home"><BF008.txt></span><span id="cid:CD9D7E24-3DFB-461D-995B-24AF00A0E92C@Home"><BF008-bf.tiff></span><span id="cid:95517BA5-4497-4B43-8DDF-2346AB1777EE@Home"><BF008-Capture
du 2017-08-13 18-50-53.png></span><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="">
<span id="cid:979CAD29-3FFC-45D0-AEA3-C1D60E5DA646@Home"><convert.log></span>- 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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</blockquote>
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