<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Enno,<div><br></div><div>at the moment, there is no easy way to downsample at the Bio-Formats level:</div><div><br></div><div>For what you want to achieve, there are two solutions:</div><div>- either you'll need to first retrieve the full plane (or the full tile) and then do the downsampling</div><div> at the MATLAB level</div><div>- alternatively, you could use openThumbBytes() to retrieve a thumbnail:</div><div> <a href="http://downloads.openmicroscopy.org/bio-formats/5.0.2/api/loci/formats/FormatReader.html#openThumbBytes(int)">http://downloads.openmicroscopy.org/bio-formats/5.0.2/api/loci/formats/FormatReader.html#openThumbBytes(int)</a></div><div> Note that in this case, you also do not have any control on the downsampling factor</div><div> and the method above will return a byte array which you'll need to convert.</div><div><br></div><div>Best,</div><div>Sebastien </div><div><br><div><div>On 29 Jul 2014, at 15:54, Enno R. Oldewurtel <<a href="mailto:enno.oldewurtel@uni-koeln.de">enno.oldewurtel@uni-koeln.de</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div><div>Hi Sebastien,<br></div>is it possible to not only crop, but also downsample when reading an nd2 file? Using the PixelRegion Parameter when reading in tif files via matlab's imread function, one can also specify an increment. This is useful for me when I quickly want to display a very large image for overview, where it is sufficient to only see every 5th pixel or so.<br>
<br></div><div>On another note, the 5.0.2-DEV version is more than a factor of two faster executing r.setID for nd2 files on my system, which is very much appreciated by me!<br></div><div><br>
</div>Thanks,<br>Enno<br><div><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 28, 2014 at 2:52 PM, Enno R. Oldewurtel <span dir="ltr"><<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Sebastien,<br></div>the 5.0.2-DEV version you pointed me to works and bfopen returns a correctly cropped image.<br>
</div>Best wishes,<br></div>Enno<br></div><div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Mon, Jul 28, 2014 at 2:19 PM, Sebastien Besson <span dir="ltr"><<a href="mailto:seb.besson@gmail.com" target="_blank">seb.besson@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Enno,<div><br></div><div>thanks for the quick upload. I have been able to reproduce the bug you saw using MATLAB</div><div>and Bio-Formats 5.0.2 and I can confirm the 5.0.3 release candidate should fix this issue with</div>
<div>the tile correctly loaded.</div><div><br></div><div>You can either wait for the imminent 5.0.3 release of try out one of the non-release</div><div>quality continuous integration artifacts from:</div><div><a href="http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/" target="_blank">http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/</a></div>
<div><br></div><div>Best regards,</div><div>Sebastien</div><div><br><div><div>On 28 Jul 2014, at 13:10, Enno R. Oldewurtel <<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div><div><div>Hey Sebastien,<br><br></div>I used the 5.0.2 release. I uploaded a nd2 file as requested<br><a href="http://qa.openmicroscopy.org.uk/qa/feedback/9422/?token=f74e8565db4a90d1b876660e6b2e3e21" target="_blank">http://qa.openmicroscopy.org.uk/qa/feedback/9422/?token=f74e8565db4a90d1b876660e6b2e3e21</a><br>
</div><br></div>Thanks for the quick reply,<br>Enno<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 28, 2014 at 1:44 PM, Sebastien Besson <span dir="ltr"><<a href="mailto:seb.besson@gmail.com" target="_blank">seb.besson@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Enno,<div><br></div><div>which version of Bio-Formats are you using? The upcoming 5.0.3 release of Bio-Formats</div>
<div>will include a large set of bug fixes for the ND2 format.</div><div>Could you upload a sample file to <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a> for us to check</div>
<div>this release also addresses your issues?</div><div><br></div><div>Best regards,</div><div>Sebastien</div><div><br><div><div><div>On 28 Jul 2014, at 12:19, Enno R. Oldewurtel <<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>> wrote:</div>
<br></div><blockquote type="cite"><div dir="ltr"><div><div>Dear all,<br><br></div><div>I just tried to read in ND2 files via matlab (either using r.openBytes directly or bfopen.m). However, when specifying a sub-image with x-origin>=2, the resulting image is skewed along a diagonal with slope depending on the x-origin, i.e. slope=1 for x-origin=2. The y-origin works with all values.<br>
<br>This is the command I use:<br>test=bfopen(f,2,1,400,300);<br><br></div><div>Using bfopen on a tif-file returns a correctly cropped image. Thus this might be a nd2 specific problem.<br><br></div><div>Has anyone experienced the same problem?<br>
<br></div></div><div>These are images obtained with x-origin=1 and x-origin=2:<span><x-originEquals1.png></span><span><x-originEquals2.png></span><br>
</div><div><div><br></div><div>Thanks,<br>Enno<br></div><div><br></div><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>
50674 Koeln<br>
<br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br><a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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</blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>50674 Koeln<br>
<br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>Tel: <a href="tel:%2B49-221-470-8048" value="+492214708048" target="_blank">+49-221-470-8048</a><br>Fax: <a href="tel:%2B49-221-470-6230" value="+492214706230" target="_blank">+49-221-470-6230</a><br>
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</blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>
50674 Koeln<br><br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>Tel: <a href="tel:%2B49-221-470-8048" value="+492214708048" target="_blank">+49-221-470-8048</a><br>Fax: <a href="tel:%2B49-221-470-6230" value="+492214706230" target="_blank">+49-221-470-6230</a><br>
<a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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</div></blockquote></div><br><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>50674 Koeln<br><br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>
Tel: <a href="tel:%2B49-221-470-8048" value="+492214708048" target="_blank">+49-221-470-8048</a><br>Fax: <a href="tel:%2B49-221-470-6230" value="+492214706230" target="_blank">+49-221-470-6230</a><br><a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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