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Hi Sebastian-<div><br></div><div>Ok, again; a few problems.</div><div><br></div><div>Many people have noted the limited exposure of metadata in OMERO.insight. The good news is that this is a subset of what is in the database-- so much of what you want is in the DB. But it is not all there-- some metadata is not supported by Bio-formats, some doesn't have a home in OMERO. </div><div><br></div><div>This is why we are (as I type) are in the middle of a "metadata completeness" iteration-- from Bio-Formats through to OMERO.insight and OMERO.editor, we are working hard to address a complete metadata workflow. This is a massive undertaking, and much of the team is focussed on it. As an example, it means going through each file format and ensuring we have a home for all metadata somewhere in OMERO. Given the huge disparity in metadata support across different vendor file formats, this takes some work. It also means finding ways to define what people want to see and how, and raises the question of what metadata is editable. We've had long discussions about this for many years, and we also have survey data coming from our partners at Usable Image. We'll provide updates on release of these facilities over the next few days.</div><div><br></div><div>It's good to hear the 510 and 710 file formats are behaving similarly-- this is helpful.</div><div><br></div><div>I'll ask Brian to follow-up on your question about Bio-Rad .PIC. </div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><div><div><div>Sebastian Cachero wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Jason,<div><br></div><div>We are having the same problem with both types of files.</div><div><br></div><div>If I open a 710 or 510 file in imageJ using bio-formats importer and the ask for the file info I get a whole bunch of metadata but after importing them into OMERO I can only see a basic set of data. </div><div><br></div><div>A second problem seems to be that the LSM software from Zeiss gives a different voxel size than the metadata retrieved by bio-formats importer/OMERO (the LSM toolbox gives the same voxel size as the LSM soft, I guess that bio-formats might be calculating voxel size differently) .</div><div><br></div><div>Lastly, is there anything special about importing the biorad PIC files? I usually have a folder with two pic files (one for each channel) and one data.raw, lse.xml and one experiment.lse files.</div><div><br></div><div>Best,</div><div><br></div><div>Sebastian </div><div><br></div><div><br><div><div>On 30 Oct 2008, at 12:23, Jason Swedlow wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "> Hi Sebastian-<div><br></div><div>These are problems we are dealing with right now (you have a number of issues, from complete metadata support to number of channels) -- the bad news is the vendors are doing various things in their file formats that we have to deal with. They tailor their software to handle the problem for their file format-- we get to do it for all of them!</div><div><br></div><div>A more detailed response will follow, but can you confirm whether the problem you are having with Zeiss is a 510 or 710 file? </div><div><br></div><div>We are having a meeting to discuss all these problems tomorrow and will report back to the community over the weekend.</div><div><br></div><div>Thanks!</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason<br><div><div><br></div><div>On 30 Oct 2008, at 12:03, Sebastian Cachero wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<div><br></div><div>We have just installed omero in the lab and are having a couple of problems while trying to import some confocal stacks from a number of different microscopes (leica sp5, zeiss 510-710, biorad). </div><div><br></div><div><div apple-content-edited="true"><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; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>1. For some reason importing of leica .lif files fails (although bioformats-importer has no trouble importing them to imageJ).</div><div><br></div><div>2. Zeiss files are imported correctly but we get only a limited amount of the metadata from the original file.</div><div><br></div><div>3. Biorad .pic files get imported but have little metadata (same as zeiss files) and the channel information is incorrect (a two channel file gets imported as 6 channels, each one looking as being one slice offset the others)</div><div><br></div><div>Any help with this will be greatly appreciated!</div><div><br></div><div>Thanks!</div><div><br></div><div>Sebastian</div><div><br></div><div>MRC Laboratory of Molecular Biology,<br>Hills Road,<br>Cambridge,<br>CB2 2QH.<br>United Kingdom.</div><div><br><span class="Apple-style-span" style="font-size: 13px; ">Office: +44 (0)1223 252944</span></div><div><span class="Apple-style-span" style="font-size: 13px; "></span></div><div><span class="Apple-style-span" style="font-size: 13px; ">Lab<span class="Apple-tab-span" style="white-space: pre; "> </span>+44 (0)1223 252943</span><br>Fax: <span class="Apple-style-span" style="font-size: 13px; ">+44 (0)1223 402310</span><br>E-mail: <a href="mailto:scachero@mrc-lmb.cam.ac.uk">scachero@mrc-lmb.cam.ac.uk</a></div><div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div><div style="margin-top: 0px; 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