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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Hi
 Perrine and Michael,</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Trying
 to answer a couple of issues raised on this thread.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Regarding
 the performance issue, similar reports began a few years ago as the size of the acquired ND2 files started to increase sharply. Bio-Formats 5.4.0 included a significant community contribution to provide a first round of performance improvement for this file
 format [1]. </span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Our
 Bio-Formats development process includes the testing of about 200 representative ND2 filesets. The largest of ND2 file tested daily (~200G) definitely exhibited slow initialization times over a shared NFS mount prior to this performance improvements:</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">sbesson@necromancer
 ~ $ for i in $(seq 1 4); do ~/bftools-5.3.0/showinf -nopix /ome/data_repo/curated/nd2/sara/Ex9\ ALADIN\ WT\ KO\ KI\ 31_07_2013.nd2 | grep Initialization; done</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 394.658s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 16.242s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 16.168s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 16.256s</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Since
 Bio-Formats 5.4.0, the initialization time was drastically reduced so that our largest ND2 samples have been reincluded into our daily test suite,
</span><span style="font-family: Arial; font-size: 14.666666984558105px; white-space: pre-wrap;" class="">see [2] for the latest run on our current test system</span><span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;" class="">:</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">$
 for i in $(seq 1 4); do ./bftools-5.7.3/showinf -nopix /ome/data_repo/curated/nd2/sara/Ex9\ ALADIN\ WT\ KO\ KI\ 31_07_2013.nd2 | grep Initialization; done</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 2.458s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 2.514s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 2.467s</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Initialization
 took 2.457s</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">To
 help further with the slowness issue, it might be useful to have more specifics about the file size, mount option and performance metrics you are experiencing on your end.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Regarding
 the new ND2 bug, thanks as always for notifying us and uploading a representative sample file. Before we initiate more investigation, our understanding from the initial message is that the faulty files have been generated by the latest version of the acquisition
 software, is that correct? If this is the case, a definite possibility is that the data saved by the new acquisition software contains breaking changes to the Nikon ND2 format which invalidate assumptions of our reader. Has this issue been independently communicated
 to Nikon? If an update to Nikon software broke your workflow, perhaps you should report it to them?</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="kix-line-break">
</span><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Keeping up with new proprietary file formats
 or new versions of them is a perpetual challenge and not something that academic funding can support. Recent community efforts to engage with vendors led to significant contributions which have helped to reduce the burden of maintaining open-source tools essential
 for the accessibility and re-usability of scientific data. [3]</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Best,</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Sebastien</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[1]
</span><a href="http://docs.openmicroscopy.org/bio-formats/5.4.0/about/whats-new.html" style="text-decoration:none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">https://docs.openmicroscopy.org/bio-formats/5.4.0/about/whats-new.html</span></a><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[2]
</span><a href="https://web-proxy.openmicroscopy.org/next-ci/job/BIOFORMATS-test-folder/7982/console" style="text-decoration:none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">https://web-proxy.openmicroscopy.org/next-ci/job/BIOFORMATS-test-folder/7982/console</span></a><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[3]
</span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" style="text-decoration:none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</span></a><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="">
</span></div>
<div>
<blockquote type="cite" class="">
<div class="">On 8 Feb 2018, at 14:59, Perrine PAUL-GILLOTEAUX <<a href="mailto:Perrine.Paul-Gilloteaux@univ-nantes.fr" class="">Perrine.Paul-Gilloteaux@univ-nantes.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">They
 do open, (we have long multi pos of about 200Gb each), but indeed you need to be patient ...</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Data
 conversion/processing /analysis takes about 1 day with Fiji.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Le
 08-02-2018 15:42, Cammer, Michael a écrit :</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
We gave up on BioFormats for opening ND2 files more than a few hundred<br class="">
MB. We now have files that are 10+ GB and they don't open, or maybe<br class="">
they do but we don't have the patience to wait. It's faster to export<br class="">
folders of TIFs from Elements and reassemble.<br class="">
We'd love to see ND2 importer working for large files.<br class="">
MICHAEL CAMMER, Sr Research Scientist, DART Microscopy Laboratory<br class="">
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York,<br class="">
NY 10016<br class="">
C: 914-309-3270<span class="Apple-converted-space"> </span><a href="mailto:Michael.Cammer@med.nyu.edu" class="">Michael.Cammer@med.nyu.edu</a><span class="Apple-converted-space"> </span><a href="http://nyulmc.org/micros" class="">http://nyulmc.org/micros</a><br class="">
[1]<span class="Apple-converted-space"> </span><a href="http://microscopynotes.com/" class="">http://microscopynotes.com/</a><span class="Apple-converted-space"> </span>[2]<br class="">
FROM: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<br class="">
ON BEHALF OF Paul-Gilloteaux Perrine<br class="">
SENT: Thursday, February 8, 2018 9:31 AM<br class="">
TO:<span class="Apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
CC:<span class="Apple-converted-space"> </span><a href="mailto:francois.paris@univ-nantes.fr" class="">francois.paris@univ-nantes.fr</a>;<br class="">
<a href="mailto:perrine.paul-gilloteaux@univ-nantes.fr" class="">perrine.paul-gilloteaux@univ-nantes.fr</a>;<span class="Apple-converted-space"> </span><a href="mailto:Isabelle.Delias@nikon.com" class="">Isabelle.Delias@nikon.com</a>;<br class="">
<a href="mailto:manon.pietri@univ-nantes.fr" class="">manon.pietri@univ-nantes.fr</a><br class="">
SUBJECT: [ome-users] Bio-Formats ND2 importer bug<br class="">
Dear Bio-Formats team,<br class="">
Im also reporting a bug on nd2 with bioformat (tested on last release<br class="">
5.7.3 snapshot and previous)<br class="">
Disabling the chunkmap option does not solve the problem.<br class="">
I ve uploaded a short example data set here:<br class="">
<a href="https://www.openmicroscopy.org/qa2/qa/feedback/20512/?token=1f4ad9c32a8ea3de4f0c34d2c4add35c" class="">https://www.openmicroscopy.org/qa2/qa/feedback/20512/?token=1f4ad9c32a8ea3de4f0c34d2c4add35c</a><br class="">
[3]<br class="">
In a few words (see my comments on the link above), time and positions<br class="">
are shuffled, while NIS element correcty read the file metadata.<br class="">
Series corresponds to time when it should be position, and time to<br class="">
what should be position.<br class="">
It only happens when there is several channels (no problem if the<br class="">
movie is 1 channel multi-t, multi pos)<br class="">
It only happens with acquisitions generated with the last version of<br class="">
NIS 4.5.0.00 (but read correctly by previous version of NIS element).<br class="">
Best regards,<br class="">
Perrine<br class="">
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=================================<br class="">
Links:<br class="">
------<br class="">
[1]<span class="Apple-converted-space"> </span><a href="http://nyulmc.org/micros" class="">http://nyulmc.org/micros</a><br class="">
[2]<span class="Apple-converted-space"> </span><a href="http://microscopynotes.com/" class="">http://microscopynotes.com/</a><br class="">
[3]<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_feedback_20512_-3Ftoken-3D1f4ad9c32a8ea3de4f0c34d2c4add35c&amp;d=DwMFAw&amp;c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&amp;r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&amp;m=wOsSGQja4TLs56sXa1P8sT_q6DdHNaWJvRr50dHM4U4&amp;s=LH49R6mHp1j5M6bwJ4YyuzFZ7TNHPps6IrWr_9OqwIs&amp;e=" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_feedback_20512_-3Ftoken-3D1f4ad9c32a8ea3de4f0c34d2c4add35c&amp;d=DwMFAw&amp;c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&amp;r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&amp;m=wOsSGQja4TLs56sXa1P8sT_q6DdHNaWJvRr50dHM4U4&amp;s=LH49R6mHp1j5M6bwJ4YyuzFZ7TNHPps6IrWr_9OqwIs&amp;e=</a><br class="">
</blockquote>
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