<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Aaron-<div><br></div><div>Just adding one comment. From our contacts with Carl Zeiss MicroImaging we've been informally told that there were no changes in the LSM 710's file formats that we needed to know about. However, these formats are very complex, and something might have slipped by.</div><div><br></div><div>As Will mentioned, the confocal list server might be a good place to post this (this was the method we used some time ago).</div><div><br></div><div>OK, climbing on soapbox:</div><div><br></div><div>The current situation-- arbitrary file formats, with essentially any metadata in any format, and no definitive community notification when things change-- will only change when customers condition their purchases on this information being provided. In an ideal world (ok, a total pipe dream), our OME-XML and Bio-Formats developers would be notified BEFORE new formats were released and provided specifications and samples. We're a long way from that, but can get there, with the community's help. If this community insists that this information will be provided, we won't be having these problems anymore.</div><div><br></div><div>Stepping down. Phew!</div><div><br></div><div>Have a great weekend.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><div><br><div><div>On 13 Nov 2009, at 17:28, Will Moore 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 Aaron,<div><br></div><div>The key question is whether the stage position metadata is actually stored in the file. If it is, then it should be possible for BioFormats to identify the correct bit of metadata and store it in the OME data model. </div><div><br></div><div>We have been working at improving the amount of metadata from these confocal formats that is used to populate the OME model. This takes time to identify how to read the piece of metadata in the original file, and how to map it into the OME model. However, we have so far been successful for the various bits of metadata we've attempted so far. </div><div><br></div><div>There are a couple of ways to determine whether the stage position metadata is actually in the file:</div><div>Open the file in the proprietary software (Olympus, Zeiss, Lecia) and see if it is displayed. </div><div>Or, open the file in ImageJ, using the BioFormats plugin and look at the "Original Metadata". </div><div><br></div><div>I've tried these with a sample of the various formats you mentioned, and I don't see that any of them have absolute stage positions. (some examples below)</div><div>I'm not even sure that BioFormats is reading the Leica stage positions properly. Haven't looked at this before. </div><div><br></div><div>However, I don't have any LSM 710 files (LSM 510 only), and it's also possible that newer versions of these microscopes might save this data. </div><div>Some of these files seem to have places in the files for this metadata, and it's also possible that the formats might expand to accommodate stage metadata. </div><div><br></div><div>You could try asking on the confocal lists <a href="http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy">http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy</a></div><div><br></div><div> Sorry I couldn't be more help,</div><div><br></div><div> Will. </div><div><br></div><div><br></div><div><br></div><div>Looking at the "original metadata" of a couple of oib files, read by Bioformats (using the ImageJ plugin). NB. This is all the "available" metadata currently read by BioFormats, only a subset of this is used to populate the OME data model. </div><div>This is the data available for each plane of the image, shown for the first 2 planes of a Z stack.</div><div><br></div><div><div><div>Image 0 : AS Level<span class="Apple-tab-span" style="white-space:pre"> </span>9999</div><div>Image 0 : AbsPositionUnitName<span class="Apple-tab-span" style="white-space:pre"> </span>mm</div><div>Image 0 : AbsPositionValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 0 : Adjust Outward<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : Adjust Retrun<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : AnalogPMTGain<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 0 : AnalogPMTOffset<span class="Apple-tab-span" style="white-space:pre"> </span>2</div><div>Image 0 : Confocal<span class="Apple-tab-span" style="white-space:pre"> </span>ON</div><div>Image 0 : CountingPMTGain<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 0 : CountingPMTOffset<span class="Apple-tab-span" style="white-space:pre"> </span>1.600000</div><div>Image 0 : CountingPMTVoltage<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : DataMax<span class="Apple-tab-span" style="white-space:pre"> </span>4095.0</div><div>Image 0 : DataMin<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 0 : DataName<span class="Apple-tab-span" style="white-space:pre"> </span>1h_after_pdt_C001Z001T001.tif</div><div>Image 0 : DataType<span class="Apple-tab-span" style="white-space:pre"> </span>WORD</div><div>Image 0 : ExcitationOutPutLevel<span class="Apple-tab-span" style="white-space:pre"> </span>5</div><div>Image 0 : HeightConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.207</div><div>Image 0 : HeightUnit<span class="Apple-tab-span" style="white-space:pre"> </span>um</div><div>Image 0 : ImageDepth<span class="Apple-tab-span" style="white-space:pre"> </span>2</div><div>Image 0 : ImageGroup<span class="Apple-tab-span" style="white-space:pre"> </span>Normal</div><div>Image 0 : ImageHeight<span class="Apple-tab-span" style="white-space:pre"> </span>1024</div><div>Image 0 : ImageType<span class="Apple-tab-span" style="white-space:pre"> </span>Intensity</div><div>Image 0 : ImageWidth<span class="Apple-tab-span" style="white-space:pre"> </span>1024</div><div>Image 0 : LUTFileName<span class="Apple-tab-span" style="white-space:pre"> </span>LUT1</div><div>Image 0 : LUTParameter<span class="Apple-tab-span" style="white-space:pre"> </span>530227280</div><div>Image 0 : LightControl<span class="Apple-tab-span" style="white-space:pre"> </span>9999</div><div>Image 0 : Magnification<span class="Apple-tab-span" style="white-space:pre"> </span>60.0</div><div>Image 0 : Name<span class="Apple-tab-span" style="white-space:pre"> </span>COFAFrameImage</div><div>Image 0 : Number<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div>Image 0 : ObjectiveLens NAValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.35</div><div>Image 0 : ObjectiveLens Name<span class="Apple-tab-span" style="white-space:pre"> </span>UPLSAPO 60X O NA:1.35</div><div>Image 0 : ObjectiveLens WDValue<span class="Apple-tab-span" style="white-space:pre"> </span>9999.0</div><div>Image 0 : Observation Mode<span class="Apple-tab-span" style="white-space:pre"> </span>LSM</div><div>Image 0 : PMTDetectingMode<span class="Apple-tab-span" style="white-space:pre"> </span>Analog</div><div>Image 0 : PMTVoltage<span class="Apple-tab-span" style="white-space:pre"> </span>830</div><div>Image 0 : Pan Scale<span class="Apple-tab-span" style="white-space:pre"> </span>2</div><div>Image 0 : Path<span class="Apple-tab-span" style="white-space:pre"> </span>.\</div><div>Image 0 : PinholeDiameter<span class="Apple-tab-span" style="white-space:pre"> </span>115000</div><div>Image 0 : PinholeScale<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div>Image 0 : PixConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 0 : PixUnit<span class="Apple-tab-span" style="white-space:pre"> </span>Intensity</div><div>Image 0 : ROIFileName<span class="Apple-tab-span" style="white-space:pre"> </span>530223744_9038484</div><div>Image 0 : Resolution<span class="Apple-tab-span" style="white-space:pre"> </span>10.0</div><div>Image 0 : RotationValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 0 : RotationValue After Clip<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : RotationValue Before Clip<span class="Apple-tab-span" style="white-space:pre"> </span>10</div><div>Image 0 : SamplingClock<span class="Apple-tab-span" style="white-space:pre"> </span>500000</div><div>Image 0 : ScanSpeed<span class="Apple-tab-span" style="white-space:pre"> </span>2.0</div><div>Image 0 : Step<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 0 : ValidBitCounts<span class="Apple-tab-span" style="white-space:pre"> </span>12</div><div>Image 0 : Version<span class="Apple-tab-span" style="white-space:pre"> </span>1.0.0.0</div><div>Image 0 : WidthConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.207</div><div>Image 0 : WidthUnit<span class="Apple-tab-span" style="white-space:pre"> </span>um</div><div>Image 0 : X Pinhole<span class="Apple-tab-span" style="white-space:pre"> </span>318</div><div>Image 0 : XPanValue<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : Y Pinhole<span class="Apple-tab-span" style="white-space:pre"> </span>-570</div><div>Image 0 : YPanValue<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 0 : ZoomValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div><br></div><div>Image 1 : AS Level<span class="Apple-tab-span" style="white-space:pre"> </span>9999</div><div>Image 1 : AbsPositionUnitName<span class="Apple-tab-span" style="white-space:pre"> </span>mm</div><div>Image 1 : AbsPositionValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 1 : Adjust Outward<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : Adjust Retrun<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : AnalogPMTGain<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 1 : AnalogPMTOffset<span class="Apple-tab-span" style="white-space:pre"> </span>3</div><div>Image 1 : Confocal<span class="Apple-tab-span" style="white-space:pre"> </span>ON</div><div>Image 1 : CountingPMTGain<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 1 : CountingPMTOffset<span class="Apple-tab-span" style="white-space:pre"> </span>1.600000</div><div>Image 1 : CountingPMTVoltage<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : DataMax<span class="Apple-tab-span" style="white-space:pre"> </span>4095.0</div><div>Image 1 : DataMin<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 1 : DataName<span class="Apple-tab-span" style="white-space:pre"> </span>1h_after_pdt_C002Z001T001.tif</div><div>Image 1 : DataType<span class="Apple-tab-span" style="white-space:pre"> </span>WORD</div><div>Image 1 : ExcitationOutPutLevel<span class="Apple-tab-span" style="white-space:pre"> </span>4</div><div>Image 1 : HeightConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.207</div><div>Image 1 : HeightUnit<span class="Apple-tab-span" style="white-space:pre"> </span>um</div><div>Image 1 : ImageDepth<span class="Apple-tab-span" style="white-space:pre"> </span>2</div><div>Image 1 : ImageGroup<span class="Apple-tab-span" style="white-space:pre"> </span>Normal</div><div>Image 1 : ImageHeight<span class="Apple-tab-span" style="white-space:pre"> </span>1024</div><div>Image 1 : ImageType<span class="Apple-tab-span" style="white-space:pre"> </span>Intensity</div><div>Image 1 : ImageWidth<span class="Apple-tab-span" style="white-space:pre"> </span>1024</div><div>Image 1 : LUTFileName<span class="Apple-tab-span" style="white-space:pre"> </span>LUT2</div><div>Image 1 : LUTParameter<span class="Apple-tab-span" style="white-space:pre"> </span>530238208</div><div>Image 1 : LightControl<span class="Apple-tab-span" style="white-space:pre"> </span>9999</div><div>Image 1 : Magnification<span class="Apple-tab-span" style="white-space:pre"> </span>60.0</div><div>Image 1 : Name<span class="Apple-tab-span" style="white-space:pre"> </span>COFAFrameImage</div><div>Image 1 : Number<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div>Image 1 : ObjectiveLens NAValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.35</div><div>Image 1 : ObjectiveLens Name<span class="Apple-tab-span" style="white-space:pre"> </span>UPLSAPO 60X O NA:1.35</div><div>Image 1 : ObjectiveLens WDValue<span class="Apple-tab-span" style="white-space:pre"> </span>9999.0</div><div>Image 1 : Observation Mode<span class="Apple-tab-span" style="white-space:pre"> </span>LSM</div><div>Image 1 : PMTDetectingMode<span class="Apple-tab-span" style="white-space:pre"> </span>Analog</div><div>Image 1 : PMTVoltage<span class="Apple-tab-span" style="white-space:pre"> </span>700</div><div>Image 1 : Pan Scale<span class="Apple-tab-span" style="white-space:pre"> </span>2</div><div>Image 1 : Path<span class="Apple-tab-span" style="white-space:pre"> </span>.\</div><div>Image 1 : PinholeDiameter<span class="Apple-tab-span" style="white-space:pre"> </span>115000</div><div>Image 1 : PinholeScale<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div>Image 1 : PixConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 1 : PixUnit<span class="Apple-tab-span" style="white-space:pre"> </span>Intensity</div><div>Image 1 : ROIFileName<span class="Apple-tab-span" style="white-space:pre"> </span>530223744_9038484</div><div>Image 1 : Resolution<span class="Apple-tab-span" style="white-space:pre"> </span>10.0</div><div>Image 1 : RotationValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div><div>Image 1 : RotationValue After Clip<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : RotationValue Before Clip<span class="Apple-tab-span" style="white-space:pre"> </span>10</div><div>Image 1 : SamplingClock<span class="Apple-tab-span" style="white-space:pre"> </span>500000</div><div>Image 1 : ScanSpeed<span class="Apple-tab-span" style="white-space:pre"> </span>2.0</div><div>Image 1 : Step<span class="Apple-tab-span" style="white-space:pre"> </span>0.0</div><div>Image 1 : ValidBitCounts<span class="Apple-tab-span" style="white-space:pre"> </span>12</div><div>Image 1 : Version<span class="Apple-tab-span" style="white-space:pre"> </span>1.0.0.0</div><div>Image 1 : WidthConvertValue<span class="Apple-tab-span" style="white-space:pre"> </span>0.207</div><div>Image 1 : WidthUnit<span class="Apple-tab-span" style="white-space:pre"> </span>um</div><div>Image 1 : X Pinhole<span class="Apple-tab-span" style="white-space:pre"> </span>318</div><div>Image 1 : XPanValue<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : Y Pinhole<span class="Apple-tab-span" style="white-space:pre"> </span>-570</div><div>Image 1 : YPanValue<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div>Image 1 : ZoomValue<span class="Apple-tab-span" style="white-space:pre"> </span>1.0</div></div></div><div><div><br></div><div>It looks like there might be some parameters for storing stage position (e.g. YPanValue) but they are not populated. </div><div>I also don't see any stage position info displayed in the Olympus software for this file, so I'm assuming that it is not stored. </div><div>However, I don't have a file format specification to hand, and it's also possible that newer microscopes might store this data. </div><div><br></div><div><br></div><div>Looking at a couple of Leica LIF files, I see that the metadata displayed by the software does not include stage position, but if I look in the exported metadata, I can see StagePosX="0" StagePosY="0" StagePosZ="0". So, the parameters exist in the file but it is not written in this case. This may be because the microscope that acquired this image was not fitted with a motorized stage? </div><div><br></div><div><br></div></div><div><br><div><div>On 13 Nov 2009, at 16:05, Ponti, Aaron wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hello</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">We are investigating the purchase of one of the following confocals: Zeiss LSM 710, Olympus FluoView 1000, and Leica SP/SP5. One of the criteria for the choice is the possibility to read stage positions from the files (using the loci/ome-xml tools). With loci_tools 4.1 it seems that reading the stage positions into the OME schema is supported for the Leica, but is not for the other two. Can anybody confirm this? Does anybody know if stage positions arestored at all in .lsm and .oib files?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>---------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Dr. Aaron C. Ponti</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Friedrich Miescher Institute for Biomedical Research</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Facility for Advanced Microscopy and Imaging</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Software development</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Maulbeerstrasse 66 CH-4058, Basel</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| WRO-1066.2.16</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Tel: +41 61 696 3513</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Fax: +41 61 697 3976</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| <a href="http://www.fmi.ch/faim">http://www.fmi.ch/faim</a></div><div style="margin-top: 0px; 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"><div>William Moore</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Division of Gene Regulation and Expression</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">College of Life Sciences</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of Dundee</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scotland</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">DD1 5PH</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; ">Tel 01382 386364</div></div></span> </div><br></div></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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-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: <a href="http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html">http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span> </div><br></div></body></html>