Hi Ellen,<div><br></div><div>Nice to hear from you!</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br><span style="color:rgb(31,73,125)">we can open files on my mac using Image J and the data viewer plugin, but this does not seem to work on PCs.</span></blockquote><div><br></div><div>We did a lot of work to make Bio-Formats able to read QuickTime movies, especially data produced by 4D Grabber. In particular, it can read QuickTime movies compressed with the codecs (Motion JPEG-A and -B) that 4D Grabber usually used. As an aside, beware that movies compressed with these codecs are no longer supported on OS X since 10.7 Lion!</div>
<div><br></div><div>So, first download Fiji (<a href="http://fiji.sc/">http://fiji.sc/</a>) and make sure it is fully up to date (Help > Update Fiji). The update process is a little rocky at the moment but should work if you run it repeatedly (restarting Fiji as needed) until the updater tells you that everything is fully up to date.</div>
<div><br></div><div>Once you have an up-to-date Fiji, run File > Import > Bio-Formats and select one of your QuickTime movies. When the options dialog appears, if you have multiple movies (e.g., for multiple focal planes), then check the "Group files with similar names" checkbox to import them all as a single 5D dataset. If the movies are too large to fit in RAM, you can also check the "Use virtual stacks" checkbox to save memory.</div>
<div><br></div><div><div>If you have a particular file that you are unable to read, and you believe it could be a bug or limitation in the Bio-Formats ImageJ plugin, you can send us the data using Fiji's Help > Upload Sample Image command.</div>
<div><br></div></div><div>Lastly, one thing to be careful of is that your old QuickTime movies are "flattened" for use on non-Macs. If you don't flatten your movies, there is no chance of any software on the destination PCs being able to read them, because key parts of the movie are stored OUTSIDE the movie file, in a special resource area on your Mac—such that when you copy the movie to the PC, not everything is actually copied!</div>
<div><br></div><div>If you aren't sure, you can open them up in QuickTime Player and then use "Save As..." to resave them in flattened form.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>Sometimes the PC can see the files but doesn’t recognize the format, and sometimes the PC detects there is data on a disk but can’t even “see” files. I wonder if it is some sort of issue with the compression ? </blockquote>
<div><br></div><div>If the PC cannot even recognize that there are files present, that is a real problem. It could be something wrong with the disk. To diagnose further, we would have to go over in more detail what kind of disks you are using (external hard drives? CDs? DVDs?), what exactly you see on the file system, etc. This may be a job better suited to your institution's technical support channels.</div>
<div><br></div><div>Otherwise, if you want to pursue further email support from the Bio-Formats team, please follow the instructions described here:</div><div> <a href="http://loci.wisc.edu/bio-formats/bug-reporting">http://loci.wisc.edu/bio-formats/bug-reporting</a></div>
<div><br></div><div>Or you can use the Fiji bug reporting mechanism:</div><div> <a href="http://fiji.sc/Report_a_Bug">http://fiji.sc/Report_a_Bug</a></div><div><br></div><div>Regards,</div><div>Curtis</div><div><br><br>
<div class="gmail_quote">On Mon, Sep 10, 2012 at 6:49 AM, Ellen Batchelder <span dir="ltr"><<a href="mailto:EBatchelder@unity.edu" target="_blank">EBatchelder@unity.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="color:#1f497d">p.s. we can open files on my mac using Image J and the data viewer plugin, but this does not seem to work on PCs. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="color:#1f497d"><u></u> <u></u></span></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<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""> Ellen Batchelder <br>
<b>Sent:</b> Monday, September 10, 2012 7:49 AM<br><b>To:</b> '<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>'<br><b>Cc:</b> Chaz James<br><b>Subject:</b> Request for help with file format<u></u><u></u></span></p>
</div></div><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Hi Chris,<u></u><u></u></p><p class="MsoNormal">I wonder if you remember me- I was a member of John White’s c. elegans lab several years back. How are things at LOCI? I looked you up to find your email address and the picture of you is with short hair… have you had it cut? I also notice the towers of Mountain Dew photos are still up… <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">The reason I am emailing is because I’m now working at Unity College in Maine, and finally starting to think about doing some research. I was interested in looking back at some of the data gathered while I was in the White lab. I’ll be working with a student who I’ve copied on this email. The data was nearly all acquired with 4D grabber on Macs. Of course, at Unity, we all use PCs. I’m wondering if you have any thoughts about converting these files to something the pc can read? They don’t need to be pretty, just viewable.<u></u><u></u></p>
<p class="MsoNormal">Sometimes the PC can see the files but doesn’t recognize the format, and sometimes the PC detects there is data on a disk but can’t even “see” files. I wonder if it is some sort of issue with the compression ? <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Any thoughts would be appreciated….<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Sincerely,<u></u><u></u></p><p class="MsoNormal">
Ellen Batchelder<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p></div></div></div></div></blockquote></div><br></div>