<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Roger,<div class=""><br class=""></div><div class="">File uploaded <span style="color: rgb(85, 85, 85); font-family: Arial, Verdana, Lucida, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);" class=""><a href="https://www.openmicroscopy.org/qa2/qa2/qa/feedback/17455/?token=0d0ad37c09cfdd73ca5c28df3d42e1b0" class="">https://www.openmicroscopy.org/qa2/qa2/qa/feedback/17455/?token=0d0ad37c09cfdd73ca5c28df3d42e1b0</a></span></div><div class=""><font color="#555555" face="Arial, Verdana, Lucida, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><font color="#555555" face="Arial, Verdana, Lucida, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">I am currently just using Metadata methods to populate my metadata. Can you point me in the right direction for adding this </span></font>TiffData that you refer to?</div><div class=""><br class=""></div><div class="">— Michael Ellis</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 1 Dec 2016, at 14:17, Roger Leigh <<a href="mailto:rleigh@dundee.ac.uk" class="">rleigh@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">On 01/12/16 10:48, Michael Ellis wrote:<br class=""><blockquote type="cite" class="">BioFormats does not seem to cope with a single OME.TIF file that contains 2 image series one with pixel type uint16 and one with pixel type uint8.<br class=""><br class="">I can create the file with no problem but both the bftools showinfo command line tool and the ImageJ BioFormats importer crash when trying to load the file.<br class=""><br class="">I realise mixing two images of different pixel types in a single OME.TIF file is somewhat bizarre. I have no actual need to do this but stumbled upon the situation whilst designing unit tests for my code.<br class=""><br class="">My questions are:<br class=""><br class="">- Is there anything else apparent from the output that points to anything wrong that I am doing?<br class="">- Is this a bug or a feature?<br class="">- If it is a feature, then where is it documented?<br class=""></blockquote><br class="">Dear Michael,<br class=""><br class="">This should work, and is certainly supported by the specification.<br class="">There are two possibilities:<br class=""><br class="">1) An outright bug in the OME-TIFF reader<br class="">2) A bug in the metadata which triggers the behaviour<br class=""><br class="">Looking at the metadata you pasted, I think a potential culprit is the<br class="">lack of "TiffData" elements in your second Image element. This likely<br class="">triggers fallback behaviour in the reader which makes it fall back to<br class="">attempting to use IFD0 as Plane0 in the image, which is of the wrong<br class="">pixel type. It's likely the case that adding TiffData elements to the<br class="">Pixels element in this image will resolve the problem.<br class=""><br class="">If the above suggestion doesn't help, if you would like to upload the<br class="">file using <a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a> I'll be happy<br class="">to look over the metadata and TIFF structure in more detail.<br class=""><br class=""><br class="">Kind regards,<br class="">Roger<br class=""><br class="">--<br class="">Dr Roger Leigh -- Open Microscopy Environment<br class="">Wellcome Trust Centre for Gene Regulation and Expression,<br class="">College of Life Sciences, University of Dundee, Dow Street,<br class="">Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br class=""><br class="">The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">_______________________________________________<br class="">ome-devel mailing list<br class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br class=""></div></div></blockquote></div><br class=""><div class="">
<div style="text-align: right;" class="">Michael Ellis (Managing Director)</div><div style="text-align: right;" class="">Digital Scientific UK Ltd.</div><div style="text-align: right;" class=""><a href="http://www.dsuk.biz" class="">http://www.dsuk.biz</a></div><div style="text-align: right;" class=""><a href="mailto:michael.ellis@dsuk.biz" class="">michael.ellis@dsuk.biz</a></div><div style="text-align: right;" class="">tel: +44(0)1223 911215</div><div style="text-align: right;" class=""><br class=""></div><div style="text-align: right;" class="">The Commercial Centre</div><div style="text-align: right;" class="">6 Green End</div><div style="text-align: right;" class="">Cambridge</div><div style="text-align: right;" class="">CB23 7DY</div>
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