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i tried setting <span style="color: rgb(55, 71, 79); font-family: Calibri;">environment variable but still i am getting the following error.</span>
<div><span style="color: rgb(55, 71, 79); font-family: Calibri;"><br>
</span></div>
<div><span style="color: rgb(55, 71, 79); font-family: Calibri;">
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">CellSensReader initializing OS-1.vsi</span></p>
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">[CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]</span></p>
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">Tile size = 512 x 512</span></p>
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;"><span style="white-space: pre;"></span>Series 0: converted 1/1 planes (100%)</span></p>
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">Tile size = 512 x 512</span></p>
<p style="margin: 0px; font: 11px Menlo; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">/opt/bftools/bf.sh: line 77:<span class="Apple-converted-space">
</span>33 Killed<span class="Apple-converted-space"> </span>java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"</span></p>
<br>
</span></div>
<div><span style="color: rgb(55, 71, 79); font-family: Calibri;">Please solve this issue. </span></div>
<div><span style="color: rgb(55, 71, 79); font-family: Calibri;">Thanks, Mohanapriya</span></div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> on behalf of David Gault (Staff) <d.gault@dundee.ac.uk><br>
<b>Sent:</b> Friday, August 24, 2018 9:51:20 AM<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] bfconvert command</font>
<div> </div>
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<div class="" style="word-wrap:break-word"><font face="Calibri" size="3" class="">Hi Mohanapriya,</font>
<div class=""><font face="Calibri" size="3" class=""><br class="">
</font></div>
<div class=""><font face="Calibri" size="3" class="">You can configure the maximum heap size for bfconvert by setting the </font><span class="" style="color:rgb(55,71,79); font-family:monospace; font-size:13.585px; font-weight:700; orphans:2; widows:2; background-color:rgb(255,255,255)">BF_MAX_MEM
</span><span class="" style="color:rgb(55,71,79); orphans:2; widows:2; background-color:rgb(255,255,255)"><font face="Calibri" size="3" class="">environment variable, the default value is 512m.</font></span></div>
<div class="" style="orphans:2; widows:2"><font color="#37474f" face="Calibri" size="3" class=""><span class="" style="background-color:rgb(255,255,255)">This can be done by setting the value before the call to bfconver, for example as below:</span></font></div>
<div class="" style="orphans:2; widows:2"><span class="" style="color:rgb(84,84,84); font-family:arial,sans-serif; font-size:small; background-color:rgb(255,255,255)"><br class="">
</span></div>
<div class="" style="orphans:2; widows:2"><span class="" style="color:rgb(84,84,84); font-family:arial,sans-serif; font-size:small; background-color:rgb(255,255,255)"><span class="x_Apple-tab-span" style="white-space:pre"></span>export </span><span class="" style="font-weight:bold; color:rgb(106,106,106); font-family:arial,sans-serif; font-size:small; background-color:rgb(255,255,255)">BF_MAX_MEM</span><span class="" style="color:rgb(84,84,84); font-family:arial,sans-serif; font-size:small; background-color:rgb(255,255,255)">=4g</span></div>
<div class=""><font face="Calibri" size="3" class=""><br class="">
</font></div>
<div class=""><font face="Calibri" size="3" class="">With Thanks,</font></div>
<div class=""><font face="Calibri" size="3" class="">David Gault</font></div>
<div class=""><font face="Calibri, Helvetica, sans-serif" size="3" class=""><br class="">
</font>
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<blockquote type="cite" class="">
<div class="">On 24 Aug 2018, at 14:34, Narapareddy, Mohanapriya <<a href="mailto:mohanapriya.narapareddy@emory.edu" class="">mohanapriya.narapareddy@emory.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div id="x_divtagdefaultwrapper" dir="ltr" class="" style="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; font-size:12pt; font-family:Calibri,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Thanks for your reply. </div>
<div class="" style="margin-top:0px; margin-bottom:0px">Can you please tell me how can i <span class="" style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px">configure how much
bfconvert can use?</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px"><br class="">
</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:15px">Thanks</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div id="x_Signature" class="">
<div class="" style="margin-top:0px; margin-bottom:0px">mohanapriya</div>
</div>
</div>
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<span class="" 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; float:none; display:inline!important"></span>
<div id="x_divRplyFwdMsg" dir="ltr" class="" 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">
<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Douglas Russell <<a href="mailto:douglas_russell@hms.harvard.edu" class="">douglas_russell@hms.harvard.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, August 23, 2018 2:23:30 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>OME User Support List<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [ome-users] Fw: bfconvert command</font>
<div class=""> </div>
</div>
<div class="" 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">
<div dir="ltr" class="">It's a Java heap space error. How much memory is available to Docker? You also might need to configure how much bfconvert can use: <a href="https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment" class="">https://docs.openmicroscopy.org/bio-formats/5.9.1/users/comlinetools/index.html#command-line-environment</a>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Douglas</div>
</div>
<br class="">
<div class="x_x_gmail_quote">
<div dir="ltr" class="">On Thu, 23 Aug 2018 at 13:32 Narapareddy, Mohanapriya <<a href="mailto:mohanapriya.narapareddy@emory.edu" class="">mohanapriya.narapareddy@emory.edu</a>> wrote:<br class="">
</div>
<blockquote class="x_x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
<div dir="ltr" class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Hello when i am trying to run the bftools dockerfile on a alpine base image i am getting the below error.</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">CellSensReader initializing OS-1.vsi</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">[CellSens VSI] -> sample-%s.tif [Tagged Image File Format]</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">Tile size = 512 x 512</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>Series 0: converted 1/1 planes (100%)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">Tile size = 512 x 512</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">Exception in thread "main" java.lang.OutOfMemoryError: Java heap space</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at java.util.Arrays.copyOf(Arrays.java:3236)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at java.io.ByteArrayOutputStream.toByteArray(ByteArrayOutputStream.java:191)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:384)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:270)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)</span></div>
<br class="">
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px">Below is my docker file. </div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">FROM alpine:3.5</span></div>
<p class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255); min-height:13px">
<span class=""> </span><br class="x_webkit-block-placeholder">
</p>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">RUN apk -Uuv add bash openjdk8-jre \</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="x_x_m_6997727838363348083Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>&& mkdir /opt \</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="x_x_m_6997727838363348083Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>&& wget<span class="x_Apple-converted-space"> </span><a href="http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip" target="_blank" class="">http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip</a><span class="x_Apple-converted-space"> </span>\</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="x_x_m_6997727838363348083Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>&& unzip bftools.zip -x '*.bat' -d /opt/ \</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="x_x_m_6997727838363348083Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>&& rm /var/cache/apk/*</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255); min-height:13px">
<span class=""></span><br class="">
</div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">ENV PATH $PATH:/opt/bftools/</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255); min-height:13px">
<span class=""></span><br class="">
</div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">WORKDIR /tmp</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; color:rgb(94,52,255); background-color:rgb(255,255,255)">
<span class="">~<span class="x_Apple-converted-space"> </span><span class="x_x_m_6997727838363348083Apple-converted-space"> </span></span></div>
<br class="">
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<p class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""></span></p>
Please resolve this issue. Look forward to hear from you.
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div id="x_x_m_6997727838363348083Signature" class="">
<div class="" style="margin-top:0px; margin-bottom:0px">Thanks,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Mohanapriya</div>
</div>
</div>
<hr class="" style="display:inline-block; width:809.203125px">
<div id="x_x_m_6997727838363348083divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Manuel Stritt <<a href="mailto:manuel.stritt@idorsia.com" target="_blank" class="">manuel.stritt@idorsia.com</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, August 16, 2018 10:17:29 AM</font></div>
</div>
<div dir="ltr" class="">
<div id="x_x_m_6997727838363348083divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>OME User Support List<br class="">
</font></div>
</div>
<div dir="ltr" class="">
<div id="x_x_m_6997727838363348083divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [ome-users] Fw: bfconvert command</font></div>
</div>
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class=""><span class="" style="font-size:14.6667px; float:none; display:inline">Dear Mohanapriya,</span><span class="x_Apple-converted-space"> </span><br class="">
<div class="x_x_m_6997727838363348083x_gmail_extra"><br class="">
</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">an VSI file contains one or several scenes. Each scene /series is stored in a ets file.</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">For that reason you should have a subdirectory at the location of your VSI file which is</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">names like the VSI file (with a "_" at the start and end). Probably you moved/copied the</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">VSI file but not the corresponding ets subdirectory.</div>
<div class="x_x_m_6997727838363348083x_gmail_extra"><br class="">
</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">Regards,</div>
<div class="x_x_m_6997727838363348083x_gmail_extra">Manuel</div>
<div class="x_x_m_6997727838363348083x_gmail_extra"><br class="">
</div>
<div class="x_x_m_6997727838363348083x_gmail_extra"><br class="">
<div class="x_x_m_6997727838363348083x_gmail_quote">
<blockquote class="x_x_m_6997727838363348083x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
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<div id="x_x_m_6997727838363348083x_m_4816580915808717552divtagdefaultwrapper" dir="ltr" class="" style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Hello Josh,</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">i have done the change to "%s" and executed again but i still getting the same result.</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">bf@fc435e6036f7:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi sample1-%s.tif</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">OS-1.vsi</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">CellSensReader initializing OS-1.vsi</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="" style="background-color:rgb(255,255,0)">Missing expected .ets files in /home/bf/data/_OS-1_</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">[CellSens VSI] -> sample1-%s.tif [Tagged Image File Format]</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="white-space:pre-wrap"></span>Converted 1/1 planes (100%)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">[done]</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class="">5.339s elapsed (35.0+4022.0ms per plane, 1267ms overhead)</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><br class="">
</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><br class="">
</span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="font-size:12pt">can u please let me know </span></span></div>
<div class="" style="margin:0px; font-style:normal; font-variant:normal; font-weight:normal; font-size:11px; line-height:normal; font-family:Menlo; background-color:rgb(255,255,255)">
<span class=""><span class="" style="font-size:12pt">"</span><span class="" style="font-family:Menlo; font-size:12pt">Missing expected .ets files in /home/bf/data/_OS-1_" what does this mean</span></span></div>
<br class="">
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px">Look forward to hear from you.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Thanks,</div>
<div id="x_x_m_6997727838363348083x_m_4816580915808717552Signature" class="">
<div class="" style="margin-top:0px; margin-bottom:0px">Mohanapriya</div>
</div>
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<div id="x_x_m_6997727838363348083x_m_4816580915808717552divRplyFwdMsg" dir="ltr" class="">
<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Josh Moore <<a href="mailto:josh@glencoesoftware.com" target="_blank" class="">josh@glencoesoftware.com</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Thursday, August 16, 2018 4:04:22 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>OME User Support List<br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span>Narapareddy, Mohanapriya<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [ome-users] Fw: bfconvert command</font>
<div class=""> </div>
</div>
<div class="x_x_m_6997727838363348083x_m_4816580915808717552BodyFragment"><font size="2" class=""><span class="" style="font-size:11pt">Hi Mohan,<br class="">
<br class="">
Thanks for the details. It looks like there is a typo in the command<br class="">
line you are using in docker:<br class="">
<br class="">
bfconvert -bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br class="">
<br class="">
Here "s%" should be "%s".<br class="">
<br class="">
All the best,<br class="">
~Josh<br class="">
<br class="">
<br class="">
---------- Forwarded message ----------<br class="">
From: Narapareddy, Mohanapriya <<a href="mailto:mohanapriya.narapareddy@emory.edu" target="_blank" class="">mohanapriya.narapareddy@emory.edu</a>><br class="">
Date: Wed, Aug 15, 2018 at 8:12 PM<br class="">
Subject: Re: ome-users mailing list email<br class="">
To: Josh Moore <<a href="mailto:j.a.moore@dundee.ac.uk" target="_blank" class="">j.a.moore@dundee.ac.uk</a>><br class="">
<br class="">
<br class="">
Hello Josh Moore,<br class="">
<br class="">
Thanks for your reply.<br class="">
<br class="">
i have used java version 7 and bio formats version 5.8.2 .<br class="">
docker run -it -v ~/Desktop/dir:/home/bf/data test<br class="">
]This is my docker run<br class="">
command. and inside the container i am executing the following<br class="">
command.<br class="">
bfconvert<br class="">
-bigtiff -compression LZW OS-1.vsi sample1-s%.tif<br class="">
FROM java:7 MAINTAINER <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank" class="">ome-devel@lists.openmicroscopy.org.uk</a> RUN<br class="">
apt-get install -y curl RUN curl -o bftools.zip $(curl -Ls -o<br class="">
/dev/null -w %{url_effective}<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__downloads.openmicroscopy.org_latest_bio-2Dformats-29_artifacts_bftools.zip&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=hG980ESxUhpWXeq9BOrnOv3CUpq5lW8uGu7OdRUzoVI&m=voky8_dW4UwOtkK0WpmWnZzp7BaSnvyFxatV-lr3kbQ&s=4ETZLRNOcMDE7VxI5PFQsud3HfmoF9cG0Bnp2yPu36w&e=" target="_blank" class="">http://downloads.openmicroscopy.org/latest/bio-formats)/artifacts/bftools.zip</a><br class="">
RUN apt-get install -y unzip RUN unzip -d /opt bftools.zip && rm<br class="">
bftools.zip RUN chmod a+rx /opt/bftools/* RUN useradd -m bf USER bf<br class="">
RUN echo 'export PATH=/opt/bftools:$PATH' >> /home/bf/.bashrc ENV HOME<br class="">
/home/bf WORKDIR /home/bf CMD bash<br class="">
<br class="">
<br class="">
<br class="">
The above is my docker file.<br class="">
<br class="">
<br class="">
4. I dont see any error messages but i am getting the following out put.<br class="">
<br class="">
<br class="">
bf@935e7d25059c:~/data$ bfconvert -bigtiff -compression LZW OS-1.vsi<br class="">
sample1-s%.tif<br class="">
<br class="">
OS-1.vsi<br class="">
<br class="">
CellSensReader initializing OS-1.vsi<br class="">
<br class="">
Missing expected .ets files in /home/bf/data/_OS-1_<br class="">
<br class="">
[CellSens VSI] -> sample1-s%.tif [Tagged Image File Format]<br class="">
<br class="">
Converted 1/1 planes (100%)<br class="">
<br class="">
[done]<br class="">
<br class="">
6.95s elapsed (69.0+5815.0ms per plane, 1053ms overhead)<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
look forward to hear from you.<br class="">
<br class="">
Thanks,<br class="">
<br class="">
Mohanapriya<br class="">
<br class="">
On Tue, Aug 14, 2018 at 10:59 PM, Narapareddy, Mohanapriya<br class="">
<<a href="mailto:mohanapriya.narapareddy@emory.edu" target="_blank" class="">mohanapriya.narapareddy@emory.edu</a>> wrote:<br class="">
><br class="">
><br class="">
> mohanapriya<br class="">
><br class="">
><br class="">
><br class="">
> ________________________________<br class="">
> From: Narapareddy, Mohanapriya<br class="">
> Sent: Tuesday, August 14, 2018 4:39 PM<br class="">
> To: <a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a><br class="">
> Subject: bfconvert command<br class="">
><br class="">
><br class="">
> I am trying to execute this command<br class="">
> bfconvert -bigtiff -compression LZW <input file.vsi> <outfile>-%s.tif<br class="">
><br class="">
> its working fine in centOs , i am getting multiple image planes,<br class="">
> but when i am trying to execute in docker container i am getting only a<br class="">
> single image plane. Please resolve this issue.<br class="">
><br class="">
><br class="">
> Thanks,<br class="">
><br class="">
> Mohanapriya<br class="">
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