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Hi David,<br>
<br>
Thanks for your prompt reply and for providing tips about how to
open the image :)<br>
We are also looking for the fix as in Icy we don't provide access to
Bio-Formats advanced options for users ;)<br>
<br>
Best regards,<br>
<br>
- Stephane<br>
<br>
<br>
<div class="moz-cite-prefix">Le 08/02/2018 à 11:44, David Gault
(Staff) a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:601DE679-0903-4752-A642-32F7330C2636@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<p style="box-sizing: border-box; margin-bottom: 16px; color:
rgb(36, 41, 46); orphans: 2; widows: 2; background-color:
rgb(255, 255, 255); margin-top: 0px !important;" class="">
Hi Stephane,</p>
<p style="box-sizing: border-box; margin-top: 0px; margin-bottom:
16px; color: rgb(36, 41, 46); orphans: 2; widows: 2;
background-color: rgb(255, 255, 255);" class="">
Thanks for getting in touch and providing a sample file allowing
to reproduce. I can definitely confirm that with the latest
Bio-Formats release only a single image is read and that
exceptions are reported with previous versions. Bio-Formats has
recently introduced an option in the Nikon ND2 reader to make
use of the available chunkmap in order to speed up the reader
initialization notably for very large Nikon ND2 files. Although
this change has been tested against all Nikon ND2 files in our
data repository, we have received reports of issues caused by
this change. We are continuing to make improvements to this
behaviour but as an immediate workaround, disabling the chunkmap
processing should restore the correct dimensionality. </p>
<p style="box-sizing: border-box; margin-top: 0px; margin-bottom:
16px; color: rgb(36, 41, 46); orphans: 2; widows: 2;
background-color: rgb(255, 255, 255);" class="">
In FIJI you can do this by disabling the following option:</p>
<div class="">Plugins -> Bio-Formats -> Bio-Formats Plugins
Configuration -> Formats -> Nikon ND2 -> Disable
Chunkmap option</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Or using the Bio-Fomrats Java library you can
disable it as below:</div>
<div class=""><span style="font-family: SFMono-Regular, Consolas,
'Liberation Mono', Menlo, Courier, monospace; font-size:
11.9px; line-height: inherit; color: rgb(36, 41, 46); orphans:
2; widows: 2;" class=""><br class="">
</span></div>
<div class=""><span style="font-family: SFMono-Regular, Consolas,
'Liberation Mono', Menlo, Courier, monospace; font-size:
11.9px; line-height: inherit; color: rgb(36, 41, 46); orphans:
2; widows: 2;" class="">DynamicMetadataOptions options = new
DynamicMetadataOptions();</span></div>
<div class=""><span style="font-family: SFMono-Regular, Consolas,
'Liberation Mono', Menlo, Courier, monospace; font-size:
11.9px; line-height: inherit; color: rgb(36, 41, 46); orphans:
2; widows: 2;" class="">options.setBoolean("nativend2.chunkmap",
false);</span></div>
<div class=""><span style="font-family: SFMono-Regular, Consolas,
'Liberation Mono', Menlo, Courier, monospace; font-size:
11.9px; line-height: inherit; color: rgb(36, 41, 46); orphans:
2; widows: 2;" class="">reader.setMetadataOptions(options);</span></div>
<div class="">
<div class=""><br class="">
</div>
</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
</div>
<div>
<blockquote type="cite" class="">
<div class="">On 7 Feb 2018, at 14:37, Stephane Dallongeville
<<a href="mailto:stephane.dallongeville@pasteur.fr"
class="" moz-do-not-send="true">stephane.dallongeville@pasteur.fr</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Bio-Formats team,<br class="">
<br class="">
One of our users reported an issue while opening a .ND2 file
you can find here :<br class="">
<br class="">
<a
href="https://drive.google.com/file/d/1DL51ncu83ET_VQgCEXDW5j6bY0jET_XX/view?usp=sharing"
class="" moz-do-not-send="true">https://drive.google.com/file/d/1DL51ncu83ET_VQgCEXDW5j6bY0jET_XX/view?usp=sharing</a><br
class="">
<br class="">
The dataset is supposed to be a time lapse but with recents
Bio-formats releases it opens as a single image (sizeT = 1).<br
class="">
I tested with older bio-formats versions (mayeb 2 year ago)
and the dataset was opening correctly (complete timelaps)<br
class="">
With some more recents versions (1 year ago) the ND2 reader
was throwing a Negative Index Exception.<br class="">
<br class="">
Hope it helps to fix the issue :)<br class="">
<br class="">
Best,<br class="">
<br class="">
-- <br class="">
Stephane Dallongeville<br class="">
Unité d'Analyse d'Images Biologiques<br class="">
CNRS UMR 3691<br class="">
Institut Pasteur<br class="">
25 rue du Dr. Roux<br class="">
75724 Paris cedex 15 (FRANCE)<br class="">
<br class="">
Tel: +33 (0)1 45 68 87 01<br class="">
Fax: +33 (0)1 40 61 33 30<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://www.bioimageanalysis.org/">http://www.bioimageanalysis.org/</a><br class="">
<br class="">
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class="">
</div>
</blockquote>
</div>
</blockquote>
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