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<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div>Indeed it looks like the updated OpenSPIM writes files bigger than 4GB, the metadata also looks correct for me.</div><div><br></div><div>Regards,</div><div>Monika</div><div><br></div><div>W dniu .01.2016 o 12:18 HongKee Moon <moon@mpi-cbg.de> pisze:<br></div><br><blockquote style="margin: 0 0 0.80ex; border-left: #0000FF 2px solid; padding-left: 1ex">Hi Bill,<div class=""><br class=""></div><div class="">I think SPIMAcquistion was intended to be compatible with Fiji seamlessly. That is why it uses OME TIFF package.</div><div class="">Recently, we have updated SPIMAcquisition before Christmas in order to support HDF5 export and fix Anti-Drift.</div><div class="">The update contains the fix for “over 4GB tiffs” too.</div><div class="">Please, update and give it a try.</div><div class=""><br class=""></div><div class="">For the z-space, you can specify z-space and click “stack at this Z plus:”.</div><div class="">Each stack contains the z-space based on what you enter.</div><div class="">The pixel calibration is also crucial for having the correct Metadata which will be read by image readers in Fiji.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="F6DF7F64-640C-489F-BF06-D4C9C0A91D90" height="229" width="741" apple-width="yes" apple-height="yes" src="cid:353307FA-9548-457D-8511-84C62ED1026E@mpi-cbg.de" class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thank you for your comments.</div><div class="">Please, let us know if you have any feature request and/or feedback.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">HongKee</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 12, 2016, at 7:03 PM, Bill Whitney <<a href="mailto:whitnewn@clarkson.edu" class="">whitnewn@clarkson.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I have discovered that if I image a Z-stack using Micro-Manager's multi-D acquisition, the TIFF file generated differs from what I get if I image the Z-stack using SPIMAcquisition.<div class=""><br class=""></div><div class="">Here is what I have discovered so far:</div><div class=""><ul class=""><li class="">MM's Multi-D acquisition uses a micro-manager package, namely org.micromanager.acquisition.TaggedImageStorageMultipageTiff, which implements the interface org.micromanager.api.TaggedImageStorage</li><li class="">OpenSPIM uses packages from OME (Open Microscopy Environment), including loci.formats.IFormatWriter, loci.formats.ImageWriter, loci.common.services.ServiceFactory, loci.formats.MetadataTools, etc.</li><li class="">The two packages write metadata to the TIFF file differently. The main difference that is impacting me right now is the metadata for the physical space separation between Z slices. Both packages arguably write "CORRECT" metadata to the TIFF file, but in different ways. When I read the file in later using ImageJ, or the ImageJ plugin BigDataViewer, the z-spacing info is read correctly for the MM Multi-D file. However, when I try to read in a file created using SPIMAcquisition, ImageJ always thinks the z-spacing is 1 cm (when typically it is 3-5 micrometers). </li><li class="">The two packages also behave differently for LARGE files. The definition of the TIFF file format limits files to no more than 4GB. When MM's Multi-D code encounters a file that would be over the 4GB limit, it breaks it up into multiple files, each less than 4GB. SPIMAcquisition does not do anything different for files over the 4GB limit, which results in an error from the OME package. The OME package does support large files via switching from TIFF format to BIGTIFF format, but the calling code has to specify that. I was able to customize the SPIM code to do this, but the resulting BIGTIFF file proved to be unusable in ImageJ. <br class=""></li></ul><div class="">In both of these cases, the MM Multi-D behavior matches my needs, whereas the SPIMAcquisition behavior is causing me problems that I have to fix, or workaround in some way. I have been using the SPIM because we have a SPIM microscope, and we need support for a stage that can rotate in Theta, as well as move in X, Y, and Z. </div></div><div class=""><br class=""></div><div class="">I am posting this first to the SPIM group, although I know this issue involves interfaces between several groups: SPIM, Micro-manager, OME, ImageJ, etc.</div><div class=""><br class=""></div><div class="">I would like to ask the SPIM people if there was a reason for using the OME package for writing TIFF files rather than the MM package?</div><div class="">Because -- I am thinking of customizing my version of the SPIM code to use the MM package instead.</div><div class=""><br class=""></div><div class="">I appreciate thoughts on the reasonableness of doing this customization to the TIFF writing code in SPIM.</div><div class="">I also appreciate any other suggestions people have about better ways to move forward.</div><div class=""><br class=""></div><div class="">I am using the following versions at the moment:</div><div class=""> - Micro-Manager: 1.4.23 20151021</div><div class=""> - ImageJ: 1.50b</div><div class=""> - OpenSPIM: Not sure how to determine this. We originally downloaded the OpenSPIM/Fiji package. I just checked the OpenSPIM downloads page, and it is still listing a download dated 4/26/2015, so that must be the one we used. </div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Bill Whitney</div></div>
_______________________________________________<br class="">OpenSPIM mailing list<br class=""><a href="mailto:OpenSPIM@openspim.org" class="">OpenSPIM@openspim.org</a><br class="">http://openspim.org/mailman/listinfo/openspim<br class=""></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><span class="Apple-style-span" style="border-collapse: separate; line-height: normal; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class=""><br class="Apple-interchange-newline">--</div><div class="">HongKee Moon</div><div class="">Software Engineer</div><div class="">Scientific Computing Facility</div><div class=""><br class=""></div><div class="">Max Planck Institute of Molecular Cell Biology and Genetics</div><div class="">Pfotenhauerstr. 108</div><div class="">01307 Dresden</div><div class="">Germany</div><div class=""><br class=""></div><div class="">fon: +49 351 210 2740</div><div class="">fax: +49 351 210 1689</div><div class=""><a href="http://www.mpi-cbg.de" class="">www.mpi-cbg.de</a></div></span></div></span></div></span></div></span></div></span></div></div>
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<br class=""></div></blockquote><br><br><br><div id="M2Signature"><div>-- </div><div>Dr Monika Pawłowska<br>Nencki Institute<br>02-093 Warsaw<br>Pasteura 3<br>Poland</div></div></body></html>