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Hi David,<br>
<br>
up to now the Chunkmap option was ticked. I unticked it and now
Bio-Formats opens 6.8GB instead of 2GB (screenshot attached,
ComparisonChunkmap). This also results in 874 timestamps instead of
256 and the first timestamp actually starts at 0s instead of 84s
(screenshot attached, ComparisonTimestamp). It is very close now,
but the original file has 7.2GB and 1200 timestamps (we took a
picture every 100ms for 2min).<br>
<br>
Thank you for your help!<br>
<br>
Best<br>
<br>
Anna-Lena<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 24.08.2018 um 19:11 schrieb David
Gault (Staff):<br>
</div>
<blockquote type="cite"
cite="mid:3B160E28-673E-4F43-B33C-8941B312C7F7@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Ann-Lena,
<div class=""><br class="">
</div>
<div class="">What is the dimension size you are seeing when you
open the file with Bio-Formats?</div>
<div class=""><br class="">
</div>
<div class="">Does the same behaviour occur with and without the
ND2 chunk map option selected?</div>
<div class="">This can be set in: <b class="">Plugins >
Bio-Formats > Bio-Formats Plugins Configuration >
Formats > Nikon ND2 > Chunkmap</b></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 24 Aug 2018, at 00:09, Anna-Lena Merten
<<a href="mailto:anna-lena.merten@fau.de" class=""
moz-do-not-send="true">anna-lena.merten@fau.de</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 Romain,</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="">thank
you for your quick reply!</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="">As
you can see in the attached screenshot, there should be
enough RAM available for ImageJ.</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="">I
tried using the virtual stack option (Plugins ->
Bio-Formats -> Bio-Formats Importer, ticked the box
'Use virtual stack' in the dialog box), but the same
problem occurs.</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="">Best
regards,</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="">Anna-Lena</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="">
<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="">Am
23.08.2018 um 16:45 schrieb Josh Moore:</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="">
<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="">
CC Anna-Lena since she was previously not on the list.<br
class="">
~J.<br class="">
<br class="">
On Thu, Aug 23, 2018 at 8:20 AM Romain Guiet <<a
href="mailto:romain.guiet@epfl.ch" class=""
moz-do-not-send="true">romain.guiet@epfl.ch</a>>
wrote:<br class="">
<blockquote type="cite" class="">Hi Anna-Lena,<br
class="">
<br class="">
<blockquote type="cite" class="">ImageJ only indicates
2GB but does not respond with an error message<br
class="">
</blockquote>
How much RAM have you set for your ImageJ (EDIT >
Options > Memory & Threads) ?<br class="">
If you want to open the whole 7 Gb file, it should be
(at least) more than 8 GB even 12GB (if you computer
can offered it)<br class="">
<br class="">
Alternatively, you could use the virtual stack option,
just to verify if bio-formats can read all the slice.<br
class="">
<br class="">
Best,<br class="">
<br class="">
Romain<br class="">
<br class="">
<br class="">
---------------------------------------------------------------<br
class="">
Dr. Romain Guiet<br class="">
Bioimaging and Optics Platform (PT-BIOP)<br class="">
Ecole Polytechnique Fédérale de Lausanne (EPFL)<br
class="">
Faculty of Life Sciences<br class="">
Station 19, AI 0140<br class="">
CH-1015 Lausanne<br class="">
<br class="">
Phone: [+4121 69] 39629<br class="">
<a href="http://biop.epfl.ch/" class=""
moz-do-not-send="true">http://biop.epfl.ch/</a><br
class="">
---------------------------------------------------------------<br
class="">
<br class="">
<br class="">
-----Original Message-----<br class="">
From: ome-users
<a class="moz-txt-link-rfc2396E" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><ome-users-bounces@lists.openmicroscopy.org.uk></a>
On Behalf Of Anna-Lena Merten<br class="">
Sent: jeudi, 23 août 2018 07:57<br class="">
To: <a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br class="">
Subject: [ome-users] Bioformats only imports parts of
.nd2 file<br class="">
<br class="">
Hi everyone,<br class="">
<br class="">
using the NIS Elements software we recorded stacks of
images (time lapse, interval: 100ms, duration: 2 min,
Loops: 1201; 1 position, 1<br class="">
channel) which resulted in .nd2-files bigger than 7GB.<br
class="">
<br class="">
Bioformats 5.9.1 does not open the complete stack,
there are obviously images missing from the end of the
stack (NIS Elements still opens the whole time lapse).
Even though the files are bigger than 7GB, ImageJ only
indicates 2GB but does not respond with an error
message (screenshots in appendix). There do not seem
to be problems with files smaller than 2GB.<br
class="">
<br class="">
I am working with Windows 10, ImageJ 1.52e and Java
1.8.0_66 (64-bit).<br class="">
<br class="">
Thank you for your help!<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Anna-Lena<br class="">
<br class="">
--<br class="">
Anna-Lena Merten<br class="">
<br class="">
Institute of Medical Biotechnology<br class="">
Friedrich-Alexander-University Erlangen-Nuremberg
Ulrich-Schalk-Str.3, 91056 Erlangen, Germany<br
class="">
<br class="">
phone: +49 9131 85 69643<br class="">
FAX: +49 9131 85 23002<br class="">
web: <a class="moz-txt-link-freetext" href="http://www.mbt.tf.uni-erlangen.de/">http://www.mbt.tf.uni-erlangen.de/</a><br class="">
<br class="">
_______________________________________________<br
class="">
ome-users mailing list<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br
class="">
</blockquote>
</blockquote>
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
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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="">--<span
class="Apple-converted-space"> </span></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;
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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="">Anna-Lena
Merten</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="">Institute
of Medical Biotechnology</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="">Friedrich-Alexander-University
Erlangen-Nuremberg</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="">Ulrich-Schalk-Str.3,
91056 Erlangen, Germany</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="">phone:
+49 9131 85 69643</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="">FAX:
+49 9131 85 23002</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="">web:<span
class="Apple-converted-space"> </span></span><a
href="http://www.mbt.tf.uni-erlangen.de/"
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;
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word-spacing: 0px; -webkit-text-stroke-width: 0px;"
class="" moz-do-not-send="true">http://www.mbt.tf.uni-erlangen.de/</a><br
style="font-family: Helvetica; font-size: 12px;
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orphans: auto; text-align: start; text-indent: 0px;
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class="">
<br style="font-family: Helvetica; font-size: 12px;
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<span id="cid:199C4020-1721-4ADD-AA68-B514C7CDF644@Home"><Memory.PNG></span><span
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<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Anna-Lena Merten
Institute of Medical Biotechnology
Friedrich-Alexander-University Erlangen-Nuremberg
Ulrich-Schalk-Str.3, 91056 Erlangen, Germany
phone: +49 9131 85 69643
FAX: +49 9131 85 23002
web: <a class="moz-txt-link-freetext" href="http://www.mbt.tf.uni-erlangen.de/">http://www.mbt.tf.uni-erlangen.de/</a>
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