<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Forwarding to the list.<div><span class="Apple-style-span" style="font-size: 12px; "><div><span class="Apple-style-span" style="font-size: medium;"><br></span></div></span><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Olivier Cinquin <<a href="mailto:ocinquin@uci.edu">ocinquin@uci.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">2 January 2010 05:53:47 GMT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:comments@openmicroscopy.org.uk">comments@openmicroscopy.org.uk</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>Problems and suggestions about OMERO</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div>Hi,<br>I am considering having my lab use OMERO to store all of our microscopy data. I have installed the server and played with the client, and I have run into problems I'd like to report. I also have suggestions for improvements.<br><br>The three major problems I found are the following:<br>- TIFF images created in ImageJ by the Bio-Formats Importer plugin from LSM files lose most of their metadata when imported into OMERO. In particular, stacks lose the z-interval, which is a major problem for us. Everything that shows up in ImageJ with "Show Info..." (microscope settings, etc.) is also lost. The OMERO ImageJ plugin does worse, as it loses the calibration altogether. The LSM files themselves import fine into OMERO with all their metadata. But we need to do some processing in ImageJ and save as TIFF before we import the data into OMERO.<br>- the image viewer within OMERO Insight is so slow it is unusable when browsing slices of large stacks (~500MB). This is with the client and server on the same machine (8-core MacPro with 16GB of RAM); the machine was otherwise idle when I tested this. ImageJ is much faster on the same stack, and I was wondering if it might be possible to add a button to get a file to open in ImageJ (I know this can be done indirectly by exporting the data file and opening it from outside the OMERO client, but that's not very convenient), or perhaps have ImageJ run within OMERO. Having ImageJ run within OMERO would be very appealing because all the plugins out there could be easily reused. Don't know if this can easily be done.<br>- on OS X, the OMERO client has problems with file selection dialogs. The list jumps to crazy places when trying to click on a file name. The dialog also appears to be missing the standard OS X shortcuts, which makes navigation very slow. Is there any way to use native OS X dialogs? I imagine that's not a Java issue because it appears that ImageJ does use native dialogs.<br><br>Some suggestions for improvements:<br>- have relationships between images. For example, I'd like to store one image and different segmentations of that image separately, but not lose the information about the relationship between them.<br>- have a "measurements" pane that appears along with image tags and attachments. "OmeroTables" might be something somewhat similar, but I haven't been able to try it yet (can't get PyTables working properly on my machine). I need to define my own types of measurements, which will be performed outside of OMERO but that I need easy access to within OMERO.<br>- the interface to get to the protocol/experiment editor is not very intuitive. Also, would it be possible to get the protocol parameters to display along with the tags and attachments, so one can quickly see what they are?<br>- cache image files on the client (I guess there are synchronization issues, but image contents are very unlikely to change so that could just be ignored as a first step). I see you have that listed in your roadmap for 4.2.<br>- have the client save the login password (or at least give the option). It doesn't matter if it's stored in an unencrypted form. It seems that forcing users to type a password everytime leads them to either use a trivial password, or reuse the same password for many different logins, both of which can be higher security risks that storing passwords locally in plain text.<br>- have a drop-in installation of the server, containing all the necessary libraries. I imagine this might greatly extend your user base, because you would then reach out to labs that don't have personnel with system administration experience.<br><br>Finally, the main concern one always has when spending lots of time entering data with a piece of software is its long-term viability. The data are stored in a completely open format of course, but still converting them for a different piece of software might be tedious. Do you have plans to keep developing OMERO in the long term, and are you expecting the funding to be sustained?<br><br>I'd like to thank you for your work, and for making it available as free software. OMERO looks extremely promising, and I am sure it will help set a new standard for experimental data organization, archiving, and sharing between labs.<br><br>Best wishes,<br>Olivier Cinquin<br>PS: all my comments apply to OMERO4.1.1 beta, running on OS X Server 10.6.2<br></div></blockquote><br></div><div><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: normal normal normal 12px/normal Helvetica; color: rgb(0, 0, 0); "><b>From: </b></font><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Olivier Cinquin <<a href="mailto:ocinquin@uci.edu">ocinquin@uci.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: normal normal normal 12px/normal Helvetica; color: rgb(0, 0, 0); "><b>Date: </b></font><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">5 January 2010 18:23:59 GMT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: normal normal normal 12px/normal Helvetica; color: rgb(0, 0, 0); "><b>To: </b></font><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Aleksandra Tarkowska <<a href="mailto:aleksandrat@lifesci.dundee.ac.uk">aleksandrat@lifesci.dundee.ac.uk</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: normal normal normal 12px/normal Helvetica; color: rgb(0, 0, 0); "><b>Subject: </b></font><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; "><b>Re: Problems and suggestions about OMERO</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></div><div>A suggestion I forgot to add is to have a "blind" view of a set of images, i.e. have OMERO show a set of images without showing the date and time of creation, the original file name, or the detail of what experimental protocol they correspond to (for example whether they correspond to treated or control samples). It might be necessary to randomize the order in which the images are listed. Users could score the features of interest blindly, and only see the results once they're through scoring all images. A related suggestion is to store all measurements on a per-user basis (i.e. allow more than one user to define the same measurement for an image), which would make it easy to see how well different users agree in their [blind] scoring.<br><br>Best wishes,<br>Olivier</div></blockquote></div><div apple-content-edited="true"><br> </div><br></body></html>