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Hi James,
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<div class="">If you download the command line tools from <a href="https://www.openmicroscopy.org/bio-formats/downloads/" class="">https://www.openmicroscopy.org/bio-formats/downloads/</a> can you reproduce the error using:</div>
<div class=""><b class="">showinf -nopix path/to/file/sample.ims</b></div>
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<div class="">Also if you are able to check the first 8 bytes of the file that would allow us to confirm the expected signature.</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 25 Jul 2018, at 09:54, WAINWRIGHT James <<a href="mailto:J.Wainwright@ANDOR.COM" class="">J.Wainwright@ANDOR.COM</a>> wrote:</div>
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<span class="">Hi David,<o:p class=""></o:p></span></div>
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<span class="">I have now repeated the problem, which is independent of using a Virtual Stack.<o:p class=""></o:p></span></div>
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<span class="">The problem happens somewhere between 57GB and 95GB – for example, a 57GB file opens fine, but the 95GB file generates the following error message:<o:p class=""></o:p></span></div>
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<span class=""><image001.png></span><span class=""><o:p class=""></o:p></span></div>
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<span class="">This is using the latest netCDF from<span class="Apple-converted-space"> </span><a href="https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp" style="color: purple; text-decoration: underline;" class="">https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</a><o:p class=""></o:p></span></div>
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<span class="">How can I provide more information on how to troubleshoot this?<o:p class=""></o:p></span></div>
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<span class="">Many thanks!<o:p class=""></o:p></span></div>
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<span class="">James<o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">James Wainwright<o:p class=""></o:p></span></b></div>
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<span style="color: rgb(28, 38, 116);" class="">Global Applications Specialist - Microscopy Systems<br class="">
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<o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Tel: <span class="Apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">+44 (0) 2890 237 126 ext. 2130<o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Skype: <span class="Apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">andor.j.wainwright<o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Mob: <span class="Apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">+44 (0) 7834 710 834<br class="">
<b class="">Web:</b> <span class="Apple-converted-space"> </span><a href="https://www.andor.com/microscopy-systems" style="color: purple; text-decoration: underline;" class="">https://www.andor.com/microscopy-systems</a><o:p class=""></o:p></span></div>
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<b class=""><span lang="EN-US" class="">From:</span></b><span lang="EN-US" class=""><span class="Apple-converted-space"> </span>David Gault (Staff) [<a href="mailto:d.gault@dundee.ac.uk" style="color: purple; text-decoration: underline;" class="">mailto:d.gault@dundee.ac.uk</a>]<span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>23 July 2018 18:54<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>row_microscopy_support <<a href="mailto:row_microscopy_support@andor.com" style="color: purple; text-decoration: underline;" class="">row_microscopy_support@andor.com</a>>; WILDE Geraint <<a href="mailto:g.wilde@andor.com" style="color: purple; text-decoration: underline;" class="">g.wilde@andor.com</a>>;
WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com" style="color: purple; text-decoration: underline;" class="">J.Wainwright@andor.com</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>-|EXT|- Re: [ome-users] Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets<o:p class=""></o:p></span></div>
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Hi James,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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In the Bio-Formats importer options there is a section labelled "Memory management”, from this if you select the option “Use Virtual Stack” then it will load each frame as required rather than reading the entire file at once.<o:p class=""></o:p></div>
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With Thanks,<o:p class=""></o:p></div>
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David Gault<o:p class=""></o:p></div>
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On 23 Jul 2018, at 15:15, WAINWRIGHT James <<a href="mailto:J.Wainwright@ANDOR.COM" style="color: purple; text-decoration: underline;" class="">J.Wainwright@ANDOR.COM</a>> wrote:<o:p class=""></o:p></div>
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Just to add that these are IMS files and that we have “patched” FIJI with the latest netCDF file with the jar from here:<o:p class=""></o:p></div>
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<a href="https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">https://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp</span></a><o:p class=""></o:p></div>
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James<o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">James Wainwright</span></b><o:p class=""></o:p></div>
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<span style="color: rgb(28, 38, 116);" class="">Global Applications Specialist - Microscopy Systems<br class="">
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</span><o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Tel: <span class="apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">+44 (0) 2890 237 126 ext. 2130</span><o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Skype: <span class="apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">andor.j.wainwright</span><o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(28, 38, 116);" class="">Mob: <span class="apple-converted-space"> </span></span></b><span style="color: rgb(28, 38, 116);" class="">+44 (0) 7834 710 834<br class="">
<b class="">Web:</b> <span class="apple-converted-space"> </span><a href="https://www.andor.com/microscopy-systems" style="color: purple; text-decoration: underline;" class="">https://www.andor.com/microscopy-systems</a></span><o:p class=""></o:p></div>
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<b class=""><span lang="EN-US" class="">From:</span></b><span class="apple-converted-space"><span lang="EN-US" class=""> </span></span><span lang="EN-US" class="">row_microscopy_support<span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>23 July 2018 15:05<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">ome-users@lists.openmicroscopy.org.uk</span></a><br class="">
<b class="">Cc:</b><span class="apple-converted-space"> </span>row_microscopy_support <<a href="mailto:row_microscopy_support@andor.com" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">row_microscopy_support@andor.com</span></a>>;
WILDE Geraint <<a href="mailto:g.wilde@andor.com" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">g.wilde@andor.com</span></a>>; WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">J.Wainwright@andor.com</span></a>><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Ticket ID: 001-00-019862__Issue importing large Multi-point scans into Fiji___Doesn't occur on smaller datasets</span><o:p class=""></o:p></div>
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Hi,<o:p class=""></o:p></div>
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We have a customer in Australia that is acquiring large Multi-point datasets. Can be upwards of 500GB data sets each time.<o:p class=""></o:p></div>
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They capture full Frame, no Binning (1024x1024 pixels), dual channel ( 2 simultaneous cameras acquiring) and 60-100 Z planes on multiple X/Y positions in an overnight (timelapse) protocol. These files can be upwards of 80Gb per XY position.<o:p class=""></o:p></div>
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The problem they have is when they try and import these large data sets to FIJI it fails, however if they perform a similar experiment, only smaller in size there is no issue.<o:p class=""></o:p></div>
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After asking the customer to perform a couple of tests for us, this is what they discovered:<o:p class=""></o:p></div>
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“<b class=""><i class="">Definitely looks to be a file size issue. Tried the smaller 1.5Gb files yesterday and it worked fine. Did a longer experiment (same experimental setup just with more z-slices and more time points so the file was around 60Gb and these
are failing. The only other difference was that the small files that worked had been captured using two channel sequential while the large files that don’t work were captured with dual channel simultaneous capture.”</i></b><o:p class=""></o:p></div>
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Any advice/workaround you can supply for handling these larger datasets would be appreciated.<o:p class=""></o:p></div>
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Best,<o:p class=""></o:p></div>
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<b class="">Phil Mullan</b><br class="">
Product Support Engineer (Microscopy Systems)<br class="">
Europe, Middle East & Africa<o:p class=""></o:p></div>
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<b class="">Tel:<span class="apple-converted-space"> </span></b>+44 (0) 28 9023 7126<span class="apple-converted-space"> </span><b class="">Ext.<span class="apple-converted-space"> </span></b>2732<br class="">
<b class="">Fax:<span class="apple-converted-space"> </span></b>+44 (0) 28 9031 0792<span class="apple-converted-space"> </span><br class="">
<b class="">Web:</b> <span class="apple-converted-space"> </span><a href="http://www.andor.com/" target="_blank" style="color: purple; text-decoration: underline;" class="">andor.com/support</a><span class="apple-converted-space"> </span><br class="">
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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