<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dear OMERO developers and users,<div><br></div><div>as you know from the frequent postings from Mario Valle to this list, our OMERO / viral particle tracking project is moving along slowly but surely here in Southern Switzerland.</div><div><br></div><div>While Mario has been busy on the development side, I have spent some time test driving OMERO beta 4 from the END USER/scientist point of view.</div><div><br></div><div>First of all</div><div><br></div><div>CONGRATULATIONS on a GREAT RELEASE to all the DEVELOPERS!!!</div><div><br></div><div>This is really a quantum leap in the right direction and my feeling is that it will literally take off at the bench side in the next few months.</div><div>This is "the dawn of the age of OMERO"!</div><div><br></div><div>A part from all of these congratulatory notes, on the more useful side I would like to share a few comments I gathered after a very cursory first test drive of OMERO beta4.</div><div><br></div><div>Hope it will be useful </div><div><br></div><div>Best to all</div><div><br></div><div>Caterina</div><div><br></div><div><br></div><div><br></div><div>____________________</div><div><div><font class="Apple-style-span" face="'Times New Roman'" size="4"><span class="Apple-style-span" style="font-size: 16px;"> <!--StartFragment--> <h1>OMERO.webadmin</h1> <div class="MsoNormal">It offers basically the same functionalities of beta3 but with some great new features:</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">1. The HELP feature works well and is very useful</div> <div class="MsoNormal">2. The GROUP AMIN feature is very nice and useful, helping the ADMINISTRATOR to administer GROUP assignments of individual SCIENTISTS.</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal"> <o:p></o:p></div> <h1>OMERO.clients</h1> <div class="MsoNormal">(.importer, .insight and .editor)<o:p></o:p></div> <h2>OMERO.importer</h2> <h3>Test of import capabilities:</h3><div class="MsoNormal"><o:p></o:p></div> <div class="MsoNormal">.tiff, .stk, .lsm, .liff imported correctly in the DB</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">.lif failed</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">(The error message was reported through the DEBUG message board and also to the OME user’s listserve in a separate post).</div><div class="MsoNormal"><br></div> <h3>Importing into newly created PROJECTs and DATASETs</h3> <div class="MsoNormal">I noticed a problem during import when a new PROJECT is created by the add command in the Import Settings tab of the Import Window.</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">When a new PROJECT is added to the DB by the OMERO.importer, it is not visible in the hierarchical tree structure of DATA NAVIGATION panel of the OMERO.insight work space. The PROJECT is created but it is not visible in the tree.</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">On the other hand, when a new DATASET is added as part of a new PROJECT by the OMERO.importer, it is visible in the OMERO.insight DATA NAVIGATION panel but it appears listed at the incorrect tree depth (listed at the PROJECT depth instead than the level of DATASET). This problem does not manifest itself when a new DATASET is added as part of an existing PROJECT. </div><div class="MsoNormal"><br></div> <h2>OMERO.insight<span class="Apple-style-span" style="font-size: 19px; "></span></h2><h2><span class="Apple-style-span" style="font-size: 19px; ">General comments</span></h2> <div class="MsoNormal"> First off, CONGRATUALTIONS on a JOB well done!</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">The general comment is rally extremely positive. </div> <div class="MsoNormal">Starting from extended METADATA handling capabilities (see below on specific problems), to the new DYNAMIC WORKING AREA (I love being able to move images around on the workspace, this feature is really great to be able to sort through, classify and organize data following different and parallel criteria), the SEARCH feature, the interfacing with OMERO.editor and the HELP availability... the leap forwards is really clear and palpable.<span style="mso-spacerun: yes"> </span>This is really the way forwards!</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal"><span style="font-size:14.0pt"><b><u>Specific comments and bug-reporting<o:p></o:p></u></b></span></div> <h3>METADATA HANDLING:</h3><div class="MsoNormal"><o:p></o:p></div> <div class="MsoNormal">Metadata divided in GENERAL and ACQUISITION is very nice and useful because it allows different levels of involvement on the side of the user.</div> <ol style="margin-top:0in" start="1" type="1"> <li class="MsoNormal" style="mso-list:l2 level1 lfo1;tab-stops:list .5in">Metadata GENERAL: I like the clear and unequivocal sub-division between the COMMENTS, ATTACHMENTS and EXPERIMENTAL PROTOCOL metadata and the more technical information about the IMAGE data.</li> <li class="MsoNormal" style="mso-list:l2 level1 lfo1;tab-stops:list .5in">Metadata ACQUISITION: in general this looks great (but see some specific problems listed below).</li> </ol> <div class="MsoNormal">GENERAL PROBLEMS</div> <div class="MsoNormal">There still is an issue with being able to edit un-set or wrongly filled fields. It is not clear if more editability by user will be provided later… For now it is not available and critical METADATA information cannot be recorded. This is critical for usability.</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">Specific examples of problem areas (this is not a complete list, it is provided to give an example of the kind of problems I am talking about):</div> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l4 level1 lfo2;tab-stops:list .5in">ACQUISITION.IMAGE.ENVIRONMENT these fields have to be able to be set by user as they are rarely stored in data files</li> <li class="MsoNormal" style="mso-list:l4 level1 lfo2;tab-stops:list .5in">ACQUISITION.CHANNEL.CAMERA fields, same as above, it is useful to store but has to be filled in in many cases </li> </ul> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">INDIVIDUAL IMAGE FORMAT PROBLEMS</div> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l1 level1 lfo3;tab-stops:list .5in"><u>.stk (Metamorph)<o:p></o:p></u></li> <ul style="margin-top:0in" type="circle"> <li class="MsoNormal" style="mso-list:l1 level2 lfo3;tab-stops:list 1.0in">GENERAL fields were OK except for the "Pixel Size" field </li> <li class="MsoNormal" style="mso-list:l1 level2 lfo3;tab-stops:list 1.0in">ACQUISITION fields not populated </li></ul></ul><p class="MsoNormal" style="margin-left:.75in"><o:p></o:p></p> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l1 level1 lfo3;tab-stops:list .5in"><u>.lif (Leica) <o:p></o:p></u></li> <ul style="margin-top:0in" type="circle"> <li class="MsoNormal" style="mso-list:l1 level2 lfo3;tab-stops:list 1.0in">IMPORT FAILED (see also above)</li></ul></ul><p class="MsoNormal" style="margin-left:.25in"><o:p></o:p></p> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l1 level1 lfo3;tab-stops:list .5in"><u>.lsm (Zeiss)<o:p></o:p></u></li> <ul style="margin-top:0in" type="circle"> <li class="MsoNormal" style="mso-list:l1 level2 lfo3;tab-stops:list 1.0in">GENERAL fields were populated correctly </li> <li class="MsoNormal" style="mso-list:l1 level2 lfo3;tab-stops:list 1.0in">ACQUISITION only partially populated. Was able to differentiate correctly between a CONFOCAL channel and a transmission light channel.</li></ul></ul><div class="MsoNormal"><o:p></o:p></div> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l3 level1 lfo4;tab-stops:list .5in"><u>.tiff (various sources)<o:p></o:p></u></li> <ul style="margin-top:0in" type="circle"> <li class="MsoNormal" style="mso-list:l3 level2 lfo4;tab-stops:list 1.0in">GENERAL fields were populated correctly </li> <li class="MsoNormal" style="mso-list:l3 level2 lfo4;tab-stops:list 1.0in">ACQUISITION minimally populated, probably reflected correctly the data recorded on the file format</li></ul></ul><div class="MsoNormal"><o:p></o:p></div><p class="MsoNormal" style="margin-left:.5in;text-indent:-.25in;mso-list:l3 level1 lfo4"><span style="font-family:Symbol">·<span style="font:7.0pt "Times New Roman""> </span></span><u>.liff (OpenLab)<o:p></o:p></u></p> <ul style="margin-top:0in" type="disc"> <ul style="margin-top:0in" type="circle"> <li class="MsoNormal" style="mso-list:l3 level2 lfo4;tab-stops:list 1.0in">GENERAL fields were populated correctly </li> <li class="MsoNormal" style="mso-list:l3 level2 lfo4;tab-stops:list 1.0in">ACQUISITION minimal and sporadic, may reflect the original file format</li> </ul> </ul><p class="MsoNormal" style="margin-left:.25in"> <o:p></o:p></p> <h3>DATA ORGANIZATION</h3> <ol style="margin-top:0in" start="1" type="1"> <li class="MsoNormal" style="mso-list:l5 level1 lfo5;tab-stops:list .5in">Deleting data from DB</li> </ol><p class="MsoNormal" style="margin-left:.75in;text-indent:-.25in;mso-list:l8 level1 lfo6; tab-stops:list .75in"><span style="font-family:Symbol">·<span style="font:7.0pt "Times New Roman""> </span></span>Full deletion capabilities works nice at all tree-structure levels. This is really nice.</p> <ol style="margin-top:0in" start="2" type="1"> <li class="MsoNormal" style="mso-list:l5 level1 lfo5;tab-stops:list .5in">Data organization</li> </ol><p class="MsoNormal" style="margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo7; tab-stops:list .75in"><span style="font-family:Symbol">·<span style="font:7.0pt "Times New Roman""> </span></span>Moving between PROJECTS and DATASETS this is a working really great</p><p class="MsoNormal" style="margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo7; tab-stops:list .75in"><span style="font-family:Symbol">·<span style="font:7.0pt "Times New Roman""> </span></span>Dynamic data display on Working Area is a very nice new feature. The ability of organizing the images on the virtual workspace, will be very useful to be able to organize, classify and tag images as appropriate.</p> <div class="MsoNormal"> <o:p></o:p></div> <h3>RENDERING engine</h3> <div class="MsoNormal"><b><u>General comments<o:p></o:p></u></b></div> <div class="MsoNormal">This feature is great but still too slow for full usability.<o:p></o:p></div> <div class="MsoNormal">ROI tool is still below standard.<o:p></o:p></div> <div class="MsoNormal">This has to be clearly high on the PRIORITIES list now that beta4 is out.<o:p></o:p></div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal"><b><u>Specific problems<o:p></o:p></u></b></div><p class="MsoNormal" style="margin-left:.25in;text-indent:-.25in;mso-list:l7 level1 lfo8; tab-stops:list .25in">1.<span style="font:7.0pt "Times New Roman""> </span>I still was not able to find the facility for being able to batch-apply same RENDERING SETTINGS to entire DATASET or PROJECT.</p><p class="MsoNormal" style="margin-left:.25in">Being able to apply rendering settings across images is essential for usability.</p><p class="MsoNormal" style="margin-left:.25in">Especially CRITICAL if import fails to map the rendering colors the biologist is most used to (Green for GFP, Red for RFP etc.).</p><p class="MsoNormal" style="margin-left:.25in"><br></p><p class="MsoNormal" style="margin-left:.25in"><o:p></o:p></p><p class="MsoNormal" style="margin-left:.25in;text-indent:-.25in;mso-list:l7 level1 lfo8; tab-stops:list .25in">2.<span style="font:7.0pt "Times New Roman""> </span>Had a specific problem (BUG) when trying to copy and paste RENDERING SETTINGS from one image to another. </p><p class="MsoNormal" style="margin-left:.25in">While working on a DATASET of .lsm images the application gave an error after I copied the rendering settings and tried to paste to a new image. The error was:<span style="mso-spacerun: yes"> </span>"No Image's settings to paste". This must be a bug. </p> <div class="MsoNormal"> <o:p></o:p></div> <h3>SEARCHING</h3> <div class="MsoNormal">This feature works very nicely as far as the limited test I have done.<o:p></o:p></div> <div class="MsoNormal">Being able to fully search using attached files, OMERO.editor generated protocols, web attachments on top of comments and tags (already possible) will be critical for full usability.<o:p></o:p></div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal"><b><u>Specific comments<o:p></o:p></u></b></div> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l6 level1 lfo9;tab-stops:list .5in"><u>On a positive note</u>, a very nice feature was the ability of creating new DATASETS containing the results of the search. </li> </ul> <div class="MsoNormal"> <o:p></o:p></div> <ul style="margin-top:0in" type="disc"> <li class="MsoNormal" style="mso-list:l6 level1 lfo9;tab-stops:list .5in"><u>On a negative note</u>, Was not able to keep track of the search results when getting back to the DATA VIEWER mode.<span style="mso-spacerun: yes"> </span>It would be useful to for example highlight or somehow keep track the results once back in the DATA VIEWER in order to be able to work on the images found in the context of the remaining images. This is rendered even more difficult by the fact that in the "View as a Table" tab one does not see what PROJECT or DATASET the images belong to. The information is stored in right most panel but this is a little clumsy. </li> </ul> <div class="MsoNormal"> <o:p></o:p></div> <h3>EXPORTING</h3> <div class="MsoNormal">Nice EXPORT feature works well and is very useful for SHARING and PUBLISHING data</div> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal"> <o:p></o:p></div> <h2>OMERO.editor</h2> <div class="MsoNormal"> <o:p></o:p></div> <div class="MsoNormal">This new client has the potential for being very useful and it very well conceived. I love the ability of being able to create new protocols and also fill in parameters values when creating an EXPERIMENT from a certain protocol template. More specific comments to follow</div> <!--EndFragment--> </span></font></div></div><br><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><br class="khtml-block-placeholder"></div><div class="Letterbody"><div class="Letterbody"><div>____________________________</div><div class="MsoNormal">Caterina Strambio De Castillia, Dottore in Biologia, PhD</div><div><br></div><div>Biologiste 2 - Senior Research Scientist</div><div>Laboratory of Viral replication, pathogenesis, and immunity</div></div></div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div><a href="http://www.mimo.unige.ch/luban_lab/"></a></div><div><a href="http://www.mimo.unige.ch/luban_lab/">http://www.mimo.unige.ch/luban_lab/</a></div><div><br></div><div></div><div><div>Department of Microbiology and Molecular Medicine</div><div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 16px; margin-left: 0px; "><font style="font: normal normal normal 16px/normal Arial; "><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; ">University of Geneva<br>1 Rue Michel Servet<span class="Apple-converted-space"> </span><br>CH-1211 Geneva 4<br>Switzerland</span></font></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 16px; margin-left: 0px; "><font style="font: normal normal normal 16px/normal Arial; "><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Phone: +41-22-379-5720<br>Fax: +41-22-379-5702</span></font></font></p></div></div></div></div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">****</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Visiting Fellow</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Laboratory of Cellular and Structural Biology</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.rockefeller.edu/labheads/rout/research_project_3.php">http://www.rockefeller.edu/labheads/rout/research_project_3.php</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The Rockefeller University</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1230 York Avenue</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">New York NY 10065</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><b><span class="Apple-style-span" style="font-weight: normal; "><div>______________________________</div><div>Caterina Strambio De Castillia</div><div>via Monte Crenone 1</div><div>6500 Bellinzona </div><div>Svizzera</div><div><br class="khtml-block-placeholder"></div><div>+41 91 8252701 </div><div>+41 78 7367537</div></span></b></div></div></div></div></div><div><br class="khtml-block-placeholder"></div></div><div> </div></div></div></div></div></span></span></span></span></span></span></span></span></span></div><br></body></html>