<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nicholas-<div><br></div><div>Thanks so much for this feedback-- hugely helpful. Jean-Marie and others will be in touch with some specifics-- some of these we already have targeted, others are very useful to have.</div><div><br></div><div>Please keep all suggestions and critiques coming-- that's what makes the software better!</div><div><br></div><div>As always, thanks for your support.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br><div><div>On 31 Mar 2011, at 19:44, Nicholas Vecchietti wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Hi everybody,</font></font></span></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3"><font face="Calibri"><span></span></font></font></span><br class="webkit-block-placeholder"></div><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">I have been working with Caterina on my master project at the Microbiology Institute of Canton Ticino in Southern Switzerland and I am using OMERO quite actively.</font></font></span><span lang="EN-US"><font size="3" face="Calibri"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Using OMERO has been truly a life saver for my project allowing me to manage large numbers of images, keeping track of several experiments I am conducting in parallel and classifying images based on quality and content. </font></font></span></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3" face="Calibri"></font></span><br class="webkit-block-placeholder"></div><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">After several months of usage I have gathered a couple of comments about OMERO which I thought might be useful to share with the community.</font></font></span></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3" face="Calibri"></font></span><br class="webkit-block-placeholder"></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3" face="Calibri"></font></span><br class="webkit-block-placeholder"></div><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">In addition I have had a few problems (see below) for which I would appreciate some help.</font></font></span></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3" face="Calibri"></font></span><br class="webkit-block-placeholder"></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3" face="Calibri"></font></span><br class="webkit-block-placeholder"></div><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Comments:</font></font></span><span lang="EN-US"><font size="3" face="Calibri"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">1) In the last version of the OMERO clients (v4.2.1) I notice that the "slide show" feature was eliminated. Is there a reason why? It was very useful for rapidly comparing several images. Are you considering re-introducing this or some other tools for the purpose of comparing several images</font></font></span></p><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; "><span lang="EN-US"><font size="3"><font face="Calibri"><span></span></font></font></span><br class="webkit-block-placeholder"></div><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">2) I think it might be useful overall to add a new hierarchical level for image management which would sit below the DATA SET level allowing more flexibility in classification of image data.</font></font></span><span lang="EN-US"><font size="3"><font face="Calibri"><span> </span></font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">3) I have noticed that "comments" cannot be modified once assigned to individual images.</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">I think that it would be quite useful to consider allowing users to erase comments they have made to images as this would enable a more dynamic use of this feature.</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Would this be possible?</font></font></span><span lang="EN-US"><font size="3" face="Calibri"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Problems:</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3" face="Calibri"> </font></span><span lang="EN-US"><font size="3"><font face="Calibri">4) OMERO.insight tends to freeze after 15-20 minutes of active use. The problem gets solved by relaunching the client but this is obviously not ideal for a busy OMERO session.</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Any idea of why this is happening and how to solve it?</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3" face="Calibri"> </font></span><span lang="EN-US"><font size="3"><font face="Calibri">5) When I load single channel 8-bit tiff images acquired using the AxioVision v 4.6 driven AxioCam MRc Camera, they get imported into OMERO as three-channels images with the 3 RGB colors channels.</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3" face="Calibri"> </font></span><span lang="EN-US"><font size="3"><font face="Calibri">This is a problem as it creates an undue processing burden.</font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">Any idea as to why this might be happening?</font></font></span><span lang="EN-US"><font size="3" face="Calibri"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">In case it might help to trouble shoot the problem I can send an example image. Also, I have noticed that FIJI (which also uses BioFormats) reads the same files correctly and displays them as single 8bit images.</font></font></span><span lang="EN-US"><font size="3"><font face="Calibri"><span> </span></font></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">6) When working with .lif files from Leica, I have encountered problems with the assignment of the correct label to each individual color channels.</font></font></span><span lang="EN-US"><font size="3" face="Calibri"> </font></span></p> <div style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3"><font face="Calibri">As an example recently I have had to import .lif files containing multiple single plane images each acquired with two channels which in the Leica software I had named Leica/DAPI and LEICA/Cy3.</font></font></span></div> <div style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font face="Calibri"><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">Upon import OMERO appeared to handle these names quite inconsistently, a minority of the times the names were assigned correctly to each channel while the majority of instances both channels were assigned the name Leica/DAPI.</font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">This is obviously a problem as once imported the names are fixed and this will create considerable confusion down the line.</font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">Any idea of what is happening and how to solve it?</font></span><span lang="EN-US"><font size="3"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">Again I want to emphasize that despite these minor problems, OMERO has been really great to use and quite reliable.</font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">I hope these comments and question will contribute to make this software even more useful and widespread.</font></span><span lang="EN-US"><font size="3"> </font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">Thanks for your attention</font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">Nicholas </font></span><span lang="EN-US"><font size="3"><span> </span></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span lang="EN-US"><font size="3">-------------------------------------</font></span><span lang="EN-US"><font size="3"><span> </span></font></span></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">Nicholas Vecchietti</font></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">Istituto Cantonale di Microbiologia</font></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">Via Mirasole 22A</font></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">CH-6500 Bellinzona, Canton Ticino</font></p><p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">(Switzerland)</font></p></font></span></div> _______________________________________________<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 apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; 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