<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Moran,<div><br></div><div> You are right, you'll need to apply rendering settings to each "Dataset" in turn.</div><div>You can do this by right-clicking on an image thumbnail or on an image in the 'tree' on the left, then "Copy Settings".</div><div>Then you can right-click on each 'Dataset' in the tree and "Paste Settings".</div><div>You can also do this on the parent "Project" to apply settings to several Datasets at once.</div><div><br></div><div>I'm afraid I don't know of any documentation on how OMERO sets rendering settings on import.</div><div>In general, the min & max values are set just within the min & max pixel intensities for the image.</div><div>Channel colours can be read directly from the imported image metadata if they are specified in the file.</div><div>Let us know if you think we're missing this for a particular format.</div><div>Otherwise channel colours are chosen based on a bunch of channel metadata</div><div>Channel wavelength, emission filter wavelength etc.</div><div><br></div><div>Unfortunately the ranges are not read from the imported file into the OMERO metadata on import</div><div>so there's no way to "reset" to that original range.</div><div>However, we have started to look at fixing this limitation.</div><div><br></div><div> Regards,</div><div><br></div><div> Will.</div><div><br></div><div><br></div><div><br><div><div>On 13 Mar 2014, at 14:41, Moran Cabili-Kalmar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Ola,<div><br></div><div>so I did manage to run a version of insight that let me update the setting and do apply all- It seems like I would need to do that for each directory , correct?</div><div>Can you please point me to a documentation that explains how omero decides on the def setting of RGB, if one such exist? I am actually not sure how to set the ranges such that it which match my original image exactly.</div>
<div><br></div><div>thanks!</div><div><br></div><div>Moran</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Mar 13, 2014 at 8:47 AM, Moran Cabili-Kalmar <span dir="ltr"><<a href="mailto:nmcabili@broad.mit.edu" target="_blank">nmcabili@broad.mit.edu</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">Dear Ola,<div><br></div><div><br></div><div>Thanks so much for the quick response!</div><div>the version is <span style="line-height:18.479999542236328px;text-align:center;color:rgb(157,166,175);font-size:13px;font-family:Helvetica,Arial,sans-serif">OMERO.web 4.4.9-ice34-b98</span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">I attach the image I uploaded and a snapshot of how it appears on the web server .</span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px"> I am currently having some security problem with running insight on my computer but will try to solve this and write you back. </span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">either way I attach the image as it was uploded (this is an overlay), and provide a snapshoot for how it is displayed on the web application , which is different from the original image.</span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">if I set the red and green channel to display the max value as the maximal value in the range then I can see the correct image, but that is not seen by default, nor I was able to save this. </span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">I will need to save and apply this setting to all my images and I have a few hunderds f those.</span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">please let me know if I can provide more info.</span></font></span></div>
<div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">thanks so much!!!</span></font></span></div><span class="HOEnZb"><font color="#888888"><div>
<span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px"><br></span></font></span></div><div><span style="text-align:center"><font face="Helvetica, Arial, sans-serif" color="#000000"><span style="line-height:18.479999542236328px">moran</span></font></span></div>
</font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Mar 13, 2014 at 6:03 AM, Aleksandra Tarkowska <span dir="ltr"><<a href="mailto:A.Tarkowska@dundee.ac.uk" target="_blank">A.Tarkowska@dundee.ac.uk</a>></span> wrote:<br>
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<div>Dear Moran</div>
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<div>Which version of OMERO software do you use?</div>
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<div>Could you send us a screenshots showing the difference between Insight and Web. Both clients uses the same resources and should display images exactly in the same way.</div>
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<div>If you feel your image is imported incorrectly by default please submit original file to us and we will investigate it. You can upload it via our support system <a href="http://qa.openmicroscopy.org.uk/qa/upload" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload</a>/</div>
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<div>Kind regards</div>
<div>Ola</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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