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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Tim,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Could I ask you to elaborate on your usage of the multi-stage position in MM Multi-D? I’m setting up a 2-color SPIM, and wondered how you take your data.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In looking at the Multi-D I see that I can set different ‘z’ positions of the Twister stage. I assume you just setup a few positions with different offsets?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Also, I’m confused by the acquisition order… I’m used to seeing channel then z-position then xy location and then time lapse (for example). Is the logic reversed
in the options in MM?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If it’s easier, and you ok with it, maybe you could send a copy of your acquisition settings for me to take a look at?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks in advance for your time.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Neil<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openspim-bounces@openspim.org [mailto:openspim-bounces@openspim.org]
<b>On Behalf Of </b>Feinstein, Timothy N<br>
<b>Sent:</b> Tuesday, January 12, 2016 1:30 PM<br>
<b>To:</b> Bill Whitney; openspim@openspim.org<br>
<b>Subject:</b> Re: [OpenSPIM] Why do SPIM and Micro-Manager use different TIFF packages?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Hi Bill, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Is that necessary? We use Multi-D Acquisition because our SPIM has two lasers, and in my experience the mult-stage position mode handles sample rotation well.
Maybe I am missing something in your plan. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Best, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Tim<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Timothy Feinstein, Ph.D. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Research Scientist<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">University of Pittsburgh Department of Developmental Biology<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><<a href="mailto:openspim-bounces@openspim.org">openspim-bounces@openspim.org</a>> on behalf of Bill Whitney <<a href="mailto:whitnewn@clarkson.edu">whitnewn@clarkson.edu</a>><br>
<b>Date: </b>Tuesday, January 12, 2016 at 1:03 PM<br>
<b>To: </b>"<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>" <<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>><br>
<b>Subject: </b>[OpenSPIM] Why do SPIM and Micro-Manager use different TIFF packages?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Here is what I have discovered so far:<o:p></o:p></span></p>
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<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:10.5pt;font-family:"Calibri","sans-serif"">MM's Multi-D acquisition uses a micro-manager package, namely org.micromanager.acquisition.TaggedImageStorageMultipageTiff, which implements the interface org.micromanager.api.TaggedImageStorage<o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:10.5pt;font-family:"Calibri","sans-serif"">OpenSPIM uses packages from OME (Open Microscopy Environment), including loci.formats.IFormatWriter, loci.formats.ImageWriter, loci.common.services.ServiceFactory, loci.formats.MetadataTools,
etc.<o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:10.5pt;font-family:"Calibri","sans-serif"">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). <o:p></o:p></span></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-size:10.5pt;font-family:"Calibri","sans-serif"">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. <o:p></o:p></span></li></ul>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Because -- I am thinking of customizing my version of the SPIM code to use the MM package instead.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">I appreciate thoughts on the reasonableness of doing this customization to the TIFF writing code in SPIM.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">I also appreciate any other suggestions people have about better ways to move forward.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">I am using the following versions at the moment:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"> - Micro-Manager: 1.4.23 20151021<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"> - ImageJ: 1.50b<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"> - 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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Bill Whitney<o:p></o:p></span></p>
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