<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 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/">http://qa.openmicroscopy.org.uk/</a>.</div><div><br></div><div>Regards,</div><div>Emil<div apple-content-edited="true"><br class="Apple-interchange-newline">
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<br><div><div>On 27 Nov 2014, at 10:57, 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><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>
<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">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></div></body></html>