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Hi Mousumi,
<div class=""><br class="">
</div>
<div class="">I was simply using the standard command with no extra options:</div>
<div class=""><b class=""><font face="Consolas" style="font-size: 15px;" class="">bfconvert /path/to/input.vsi output.tiff</font></b></div>
<div class=""><br class="">
</div>
<div class="">If you are seeing issues with the memory then you can also increase it by setting <span style="font-family: Consolas; font-size: 11pt; white-space: pre-wrap;" class="">BF_MAX_MEM
</span>as below:</div>
<div class="">Mac/Linux:<b class=""> <font face="Consolas" style="font-size: 15px;" class="">export BF_MAX_MEM=4G</font></b></div>
<div class=""><span style="font-family: Consolas; font-size: 15px; white-space: pre-wrap;" class="">Windows:
<b class="">set BF_MAX_MEM=4G</b></span></div>
<div class=""><span style="font-family: Consolas; font-size: 15px; white-space: pre-wrap;" class=""><br class="">
</span></div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 23 Jun 2018, at 05:15, Mousumi Roy <<a href="mailto:mousumi.roy47@gmail.com" class="">mousumi.roy47@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi David,
<div class=""><br class="">
</div>
<div class="">Even after upgrading the Bio-format I am still not able to convert the vsi to tiff. Can you kindly specify how you are converting the vsi files? What command are you using? Even after increasing heap memory, I am getting java heap memory exception.</div>
<div class=""><br class="">
</div>
<div class="">Thank you,</div>
<div class="">Mousumi.</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">On Fri, Jun 22, 2018 at 6:27 AM David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi Mousumi,
<div class=""><br class="">
</div>
<div class="">Thank you for providing those details. With the provided sample file I am still unable to reproduce the same error using version 5.5.2.</div>
<div class=""><br class="">
</div>
<div class="">I would recommend updating to the latest Bio-Formats 5.8.2 as there have been improvements to that reader in the past number of months. If that does not fix the issue then we would likely need an additional sample file which can be used to reproduce
the error, as before it can be uploaded to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
</div>
<div style="word-wrap:break-word" class="">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 21 Jun 2018, at 19:44, Mousumi Roy <<a href="mailto:mousumi.roy47@gmail.com" target="_blank" class="">mousumi.roy47@gmail.com</a>> wrote:</div>
<br class="m_617147005674482337Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi David,
<div class=""><br class="">
</div>
<div class="">Thank you for your reply. </div>
<div class="">
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">Version: 5.5.2</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">Build date: 15 June 2017</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">VCS revision: 4c2f2b00a12aa8a3894c54459a4cf02d5b02e161</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">I am using the command:</span></p>
<div class=""><span class="m_617147005674482337inbox-inbox-s1"></span><br class="m_617147005674482337webkit-block-placeholder">
</div>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">../../bftools/bfconvert S34146_A1-Aromatase_01.vsi output.tiff </span></p>
<p class="m_617147005674482337inbox-inbox-inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-inbox-inbox-s1">(not anything else) and I am getting the following error:</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">S34146_A1-Aromatase_01.vsi</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">CellSensReader initializing S34146_A1-Aromatase_01.vsi</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">[CellSens VSI] -> output.tiff [Tagged Image File Format]</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">Switching to BigTIFF (by file size)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">Tile size = 512 x 512</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1">Exception in thread "main" java.lang.NullPointerException</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at java.lang.System.arraycopy(Native Method)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:538)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.FormatReader.openBytes(FormatReader.java:886)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.ImageReader.openBytes(ImageReader.java:441)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:698)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)</span></p>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)</span></p>
<div class=""><span class="m_617147005674482337inbox-inbox-s1"></span><br class="m_617147005674482337webkit-block-placeholder">
</div>
<p class="m_617147005674482337inbox-inbox-p1"><span class="m_617147005674482337inbox-inbox-s1"><span class="m_617147005674482337inbox-inbox-Apple-tab-span"></span>at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)</span></p>
<p class="m_617147005674482337inbox-inbox-p1">I have no clue howo should I fix this exception. Looking for your help.</p>
<p class="m_617147005674482337inbox-inbox-p1">Thank you,</p>
<p class="m_617147005674482337inbox-inbox-p1">Mousumi.</p>
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">On Thu, Jun 21, 2018 at 6:18 AM David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" target="_blank" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi Mousumi,
<div class=""><br class="">
</div>
<div class="">We received the file you uploaded and I have been able to test it with a number of different Bio-Formats versions. So far I have been unable to reproduce the error you were seeing using the command line tools. Do you know which version of Bio-Formats
you are currently using (you can find out by using <span style="font-family:Menlo;font-size:11px" class="">bfconvert -version)</span>? Are you using any other options or parameters when performing the conversion?</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
</div>
<div style="word-wrap:break-word" class="">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 20 Jun 2018, at 18:18, Mousumi Roy <<a href="mailto:mousumi.roy47@gmail.com" target="_blank" class="">mousumi.roy47@gmail.com</a>> wrote:</div>
<br class="m_617147005674482337m_8850326165244786219Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello David,
<div class=""><br class="">
</div>
<div class="">I have uploaded the .vsi and supporting files in the link. Kindly let me know if it is accessible properly. Also, I have a request to not to share this image with others.</div>
<div class=""><br class="">
</div>
<div class="">Thank you,</div>
<div class="">Mousumi.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">On Wed, Jun 20, 2018 at 10:04 AM David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" target="_blank" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi Mousumi,
<div class=""><br class="">
</div>
<div class="">Thank you for reporting the issue, this is not a bug which we are aware of with VSI, as such it would be good to have a file that reproduces the problem for testing and debugging. If you have a sample file which you can provide for testing you
can upload it to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 19 Jun 2018, at 17:09, Mousumi Roy <<a href="mailto:mousumi.roy@stonybrook.edu" target="_blank" class="">mousumi.roy@stonybrook.edu</a>> wrote:</div>
<br class="m_617147005674482337m_8850326165244786219m_8256412102395543556Apple-interchange-newline">
<div class="">
<div dir="ltr" class=""><br clear="all" class="">
<div class="">Hello,</div>
<div class=""><br class="">
</div>
<div class="">I am using bftools and trying to convert .vsi images into .tiff using
<strong class="m_617147005674482337m_8850326165244786219m_8256412102395543556gmail-command" style="color:rgb(55,71,79);font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
bfconvert</strong><span style="color:rgb(55,71,79);font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><span class=""> </span></span><span style="text-decoration:none;font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255)" class=""><a class="m_617147005674482337m_8850326165244786219m_8256412102395543556gmail-reference m_617147005674482337m_8850326165244786219m_8256412102395543556gmail-internal" href="https://docs.openmicroscopy.org/bio-formats/5.7.1/users/comlinetools/index.html" style="color:rgb(29,141,205);text-decoration:none;font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255)" target="_blank">command
line tool</a><font color="#37474f" class="">. But I am getting following error:</font></span></div>
<div class=""><em style="text-decoration:none;font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255)" class=""><font color="#37474f" class=""><strong style="box-sizing:border-box;font-weight:600;color:rgb(36,41,46);font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:14px;font-style:normal;text-align:start;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Exception
in thread "main" loci.formats.FormatException: Plane index:1 must be < 1<br style="box-sizing:border-box" class="">
at loci.formats.FormatWriter.checkParams(FormatWriter.java:387)<br style="box-sizing:border-box" class="">
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:215)<br style="box-sizing:border-box" class="">
at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)<br style="box-sizing:border-box" class="">
at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)<br style="box-sizing:border-box" class="">
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)<br style="box-sizing:border-box" class="">
at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)</strong> <br class="">
</font></em></div>
<div class=""><em style="text-decoration:none;font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px;text-align:justify;background-color:rgb(255,255,255)" class=""><font color="#37474f" class=""><br class="">
</font></em></div>
<div style="text-align:justify" class=""><font color="#37474f" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" class=""><span style="font-size:16px" class="">I have 40x .vsi files which I need to convert into .tiff format but it seems I am not
able to convert without compression. Kindly assist me.</span></font></div>
<div style="text-align:justify" class=""><font color="#37474f" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" class=""><span style="font-size:16px" class=""><br class="">
</span></font></div>
<div style="text-align:justify" class=""><font color="#37474f" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" class=""><span style="font-size:16px" class="">Thank you. Looking forward to your response.</span></font></div>
<div class=""><br class="">
</div>
Sincerely,<br class="">
<div dir="ltr" class="m_617147005674482337m_8850326165244786219m_8256412102395543556gmail_signature" data-smartmail="gmail_signature">
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<tbody class="">
<tr class="">
<td colspan="2" style="font-family:Times,Georgia,serif;padding-bottom:5px;color:rgb(247,117,31)" class="">
Mousumi Roy</td>
</tr>
<tr class="">
<td colspan="2" style="font-family:Times,Georgia,serif;color:rgb(51,51,51);font-size:12px" class="">
<i class="">Graduate Research assistant</i></td>
</tr>
<tr class="">
<td colspan="2" style="font-family:Times,Georgia,serif;color:rgb(51,51,51);font-size:12px" class="">
Computer Science</td>
</tr>
<tr class="">
<td colspan="2" style="font-family:Times,Georgia,serif;color:rgb(51,51,51);font-size:12px" class="">
<span style="font-weight:700" class="">Stony Brook University</span></td>
</tr>
<tr class="">
<td width="20" valign="top" style="font-family:Times,Georgia,serif;vertical-align:top;width:20px;color:rgb(247,117,31);font-size:12px" class="">
m:</td>
<td style="font-family:Times,Georgia,serif;color:rgb(51,51,51);font-size:12px" class="">
<a href="tel:(631)%20627-5860" value="+16316275860" target="_blank" class="">6316275860</a></td>
</tr>
<tr class="">
<td width="20" valign="top" style="font-family:Times,Georgia,serif;vertical-align:top;width:20px;color:rgb(247,117,31);font-size:12px" class="">
a:</td>
<td valign="top" style="font-family:Times,Georgia,serif;vertical-align:top;color:rgb(51,51,51);font-size:12px" class="">
<a href="https://maps.google.com/?q=100+Nicolls+Rd,+Stony+Brook,+NY+11794&entry=gmail&source=g" target="_blank" class="">100 Nicolls Rd, Stony Brook, NY 11794</a></td>
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<td width="20" valign="top" style="font-family:Times,Georgia,serif;vertical-align:top;width:20px;color:rgb(247,117,31);font-size:12px" class="">
e:</td>
<td valign="top" style="font-family:Times,Georgia,serif;vertical-align:top;color:rgb(51,51,51);font-size:12px" class="">
<a href="mailto:mousumi.roy@stonybrook.edu" style="color:rgb(29,161,219)" target="_blank" class="">mousumi.roy@stonybrook.edu</a></td>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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