<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sebastian,<div><br></div><div>That's great, thank you very much. I have created a ticket for that issue and CC'd you on it.</div><div><a href="https://trac.openmicroscopy.org.uk/ome/ticket/12673">https://trac.openmicroscopy.org.uk/ome/ticket/12673</a></div><div><br></div><div>Regards,</div><div>Emil<br><div apple-content-edited="true"><div><br></div>
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<br><div><div>On 1 Dec 2014, at 08:45, Sebastian Rhode <<a href="mailto:sebrhode@gmail.com">sebrhode@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div>Hi Emil,<br><br></div>done. I uploaded the file. Di not hesitate to contact me for info since I am really interested in solving this issue ...<br><br></div>Sebi<br></div><div class="gmail_extra"><br><div class="gmail_quote">2014-11-28 16:08 GMT+01:00 Emil Rozbicki <span dir="ltr"><<a href="mailto:emil@glencoesoftware.com" target="_blank">emil@glencoesoftware.com</a>></span>:<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"><div><div>Hi Sebastian,<div><br></div><div>I gave you a wrong link, sorry. Could you try this one: <a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank">https://www.openmicroscopy.org/qa2/qa/upload/</a></div><div><br></div><div>Cheers,</div><div>Emil<div></div></div></div><br>
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<br><div><span class=""><div>On 28 Nov 2014, at 14:03, Sebastian Rhode <<a href="mailto:sebrhode@gmail.com" target="_blank">sebrhode@gmail.com</a>> wrote:</div><br></span><blockquote type="cite"><div dir="ltr"><span class=""><div><div>Hi Emil,<br><br></div>i tried, but got an upload error...<br><br></div>Sebi<br></span><div><br><span><image.png></span><br></div></div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2014-11-28 11:29 GMT+01:00 Emil Rozbicki <span dir="ltr"><<a href="mailto:emil@glencoesoftware.com" target="_blank">emil@glencoesoftware.com</a>></span>:<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 Sebastian,<div><br></div><div>Thanks for reporting the issue. Would you mind uploading some example files that show this problem to our QA system <a href="http://qa.openmicroscopy.org.uk/" target="_blank">http://qa.openmicroscopy.org.uk/</a>.</div><div><br></div><div>Regards,</div><div>Emil<div><br>
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<br><div><div><div>On 27 Nov 2014, at 10:57, Sebastian Rhode <<a href="mailto:sebrhode@gmail.com" target="_blank">sebrhode@gmail.com</a>> wrote:</div><br></div><blockquote type="cite"><div><div dir="ltr"><div><div><div><div><div><div><div><div><div><div><div><div><div>Hi,<br><br></div>when I acquire a CZI within the ZEN software with 2 Scences, where every Scene by itself is a 2x1 Tile, the image looks like this: --> see 2 screenshots from ZEN for Scene 1 and 2.<br><br></div>There the "Acquistion order" is clear. I used the OME-Testimages with a TestCam Feature to make the images recognizable.<br><br></div>The problem is, that the BioFormtas CZIReader does no distinct dimension for Scenes and Tiles.<br></div>In ZEN inside the CZI file there is an S-Index (Scence) and M-Index(Tile).<br><br></div>The order of acquistion for the example is<br><br></div>S=0 M=0 --> Image 1<br></div>S=0 M=1 --> Image 2<br></div>S=1 M=0 --> Image 3<br></div>S=1 M=1 --> Image 4<br><br></div>But the CZIReader seems to use the M-Index as its outer loop index and the result is:<br><br>S=0 M=0 --> Image 1<br>S=1 M=0 --> Image 3<br>S=0 M=1 --> Image 2<br>S=0 M=1 --> Image 4<br><br></div>This makes is quite hard to import CZI data from for instance well images, where every well corresponds to a scence. When one uses a Tile inside a well, the BioFormat import mixes up the images and assigns images to wells, where they where not acquired.<br><br></div>Is it possible to modify the CZIReader in an way that it reads the Image Series correctly in the order of acquisition?<br><br></div>Cheers,<br><br>Sebi<br><div><br></div></div>
</div><span><CZI_Order_Test_Scene=2_Tile=2x1.czi></span><span><Scene_Image_Import_BioFormats_Problem.png></span><span><ZEN_Scene1.png></span><span><ZEN_Scene2.png></span>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br></blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br><div>Dr. Sebastian Rhode<br>Grünwalder Straße 103a<br>81547 München<br>Tel: <a href="tel:%2B49%2089%204703091" value="+49894703091" target="_blank">+49 89 4703091</a><br>Mobil: <a href="tel:%2B49%20151%2040767993" value="+4915140767993" target="_blank">+49 151 40767993</a><br><a href="mailto:sebrhode@gmail.com" target="_blank">sebrhode@gmail.com</a><br></div>
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</div></div></blockquote></div><br></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">Dr. Sebastian Rhode<br>Grünwalder Straße 103a<br>81547 München<br>Tel: +49 89 4703091<br>Mobil: +49 151 40767993<br><a href="mailto:sebrhode@gmail.com" target="_blank">sebrhode@gmail.com</a><br></div>
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