<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Juergen,<div><br></div><div>I think the problem might be 'convert'. I have the vague memory that it only works for certain bit depths of TIFF file.</div><div><br></div><div>Try using 'tiffcomment' from the Bio-Formats tools.</div><div><br></div><div><div>Usage:</div><div>tiffcomment [-set comment] [-edit] file1 [file2 ...]</div><div><br></div><div>If using the '-set' option, the new TIFF comment must be specified.</div><div>The commment may take any of the following forms:</div><div><br></div><div> * the text of the comment, e.g. 'new comment!'</div><div> * the name of the file containing the text of the comment, e.g. 'file.xml'</div><div> * '-', to enter the comment using stdin. Entering a blank line will</div><div> terminate reading from stdin.</div><div><br></div><div>So:</div><div><blockquote type="cite">convert -comment "@header_info.txt" test.tif test_new.tif</blockquote>would become something like:</div><div><blockquote type="cite">cp test.tif test_new.tif</blockquote><blockquote type="cite">tiffcomment -set 'header_info.txt' test_new.tif</blockquote></div><div><br></div><div>Hope this helps,</div><div><br></div><div>Andrew</div><div><br></div><div><br></div><div><div>On 8 Mar 2012, at 14:51, Juergen Helmers wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>I have image data from a screen using an Andor IQ2 instrument. The image data seems to be 16-bit and can be imported into Omero resulting in images with the correct number of channels (here two, red and green). <br>
<br>BUT:<br><br>The image are part of a screen of a 96 well plate. per well there are 9 ROI, each stack of multi-channel image files. What I would like to do is import the images as a screen, resulting in a plate of images incorporating the x,y information to place the images inside the grid of the 96 well plate. In addition I have setup a rails application converting CSV annoation sfile to a postgres database and I would like to add the annoation to the metadata before input. <br>
<br>this was the plan:<br><br>convert Andor tif file to OME-tif file adding the screen > plate > acquisition > well > ROI information to the header<br><br>When I try to rewrite the Exif information of any Andor file it results in a broken file:<br>
<br>exiv2 -pa test.tif > header_info.txt<br>convert -comment "@header_info.txt" test.tif test_new.tif<br><br>When I import the new tif file although the extracted and rewritten header information are identical the file when imported into Omero is a black and white single channel image. I have used this method and used software before to rewrite molecular devices files to create OME-tif files.<br>
<br>Has anyone ever dealt with Andor images in order to make them part of a screen, or has some tips on which software to use to rewrite the tif header of Andor files?<br><br>Cheers<br>Juergen<br><br clear="all"><br>-- <br>
<font><font color="#333333"><b>Dr. Juergen Helmers</b></font><br>
<i>Chief Developer</i> | webnow | <font color="#3366ff"><a href="http://www.web-now.de/" target="_blank">http://www.web-now.de</a></font><br>
<b>email:</b><a href="mailto:juergen.helmers@gmail.com" target="_blank">juergen.helmers@gmail.com</a> | <b>tel:</b>+49 30
37301306 | <b>skype:</b> helmerj </font><br>
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