<p dir="ltr">I will ask!</p>
<p dir="ltr">Best</p>
<p dir="ltr">D</p>
<div class="gmail_extra"><br><div class="gmail_quote">On 5 Oct 2016 18:08, "Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



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<span>Hi Dan,<br>
</span><span><br>
</span><span>Thanks for following up on this thread. Unfortunately we do not have any recent specification<br>
</span><span>file documenting this new Deltavision format. Without knowing the specifics, we implemented<br>
</span><span>a minimal workaround in Bio-Formats 5.2.3 released today [1] which should hopefully deliver<br>
</span><span>support for these large time-series files to the community, including your customers.<br>
</span><span><br>
</span><span>In the mid-term, updating the Bio-Formats reader to use the exact format specification is<br>
</span><span>certainly a more robust and maintainable approach as we have seen with other proprietary file<br>
</span><span>formats. In addition to the storage of the number of timepoints in the header, is there any other<br>
</span><span>major change in the specification that would affect Bio-Formats? Would you be allowed to share</span>
<div><span>part or all of this new Deltavision format specification?<br>
</span><span><br>
</span><span>Best,<br>
</span><span>Sébastien<br>
</span><span><br>
</span><span>[1] <a href="https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8133" target="_blank">https://www.<wbr>openmicroscopy.org/community/<wbr>viewtopic.php?f=11&t=8133</a></span>
<div><span><br>
</span><span><br>
</span>
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<blockquote type="cite">
<div>On 5 Oct 2016, at 09:13, Daniel White <<a href="mailto:dan@chalkie.org.uk" target="_blank">dan@chalkie.org.uk</a>> wrote:</div>
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<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm"><font color="#1f497d"><span style="font-size:10pt">Hi </span><span style="font-size:13.3333px">Bio-formats </span><span style="font-size:10pt"> folks,</span></font></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm"><font color="#1f497d"><span style="font-size:10pt">here is some more info </span><span style="font-size:13.3333px">about</span><span style="font-size:10pt"> opening
 large time </span><span style="font-size:13.3333px">series</span><span style="font-size:10pt"> .dv files, from the software engineers at the DeltaVision factory.</span></font></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">Does the latest .dv file format spec doc you have include the below info?</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">If not, let me know.</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">cheers</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">Dan</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">##############################<wbr>###################</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">There are two types of .dv formats: the old one, and the new one that we started using in 2006 which allows for much larger numbers of time-points.  From our software team,
 here’s the logic needed to determine the number of time-points in the file from the header of any .dv image file.  The complexity comes from backwards compatibility, but it should be straightforward enough!<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:36pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red">determine the image file type by reading the 16-bit integer at header byte 160<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:36pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:36pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red">if the image file type is >= 100 then<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:72pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red">determine the number of time-points from the 32-bit integer at header byte 852<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:72pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:36pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red">else if the image file type is < 100 then<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:72pt;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:11pt;font-family:calibri,sans-serif;color:red">determine the number of time-points from the 16-bit integer at header byte 180<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">If you could pass this along to the bioformats group, that would be great.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
Let me know if you/they need any more information.</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)"><br>
</span></p>
<p class="MsoNormal" style="margin-right:0cm;margin-left:0cm;font-size:12pt;font-family:"times new roman",serif">
<span style="font-size:10pt;font-family:arial,sans-serif;color:rgb(31,73,125)">##############################<wbr>####################</span></p>
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