[ome-users] Request for help with file format

[Curtis Rueden]

Hi Ellen,

Nice to hear from you!


> we can open files on my mac using Image J and the data viewer plugin, but
> this does not seem to work on PCs.


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!

So, first download Fiji (http://fiji.sc/) 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.

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.

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.

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!

If you aren't sure, you can open them up in QuickTime Player and then use
"Save As..." to resave them in flattened form.


> 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 ?


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.

Otherwise, if you want to pursue further email support from the Bio-Formats
team, please follow the instructions described here:
    http://loci.wisc.edu/bio-formats/bug-reporting

Or you can use the Fiji bug reporting mechanism:
    http://fiji.sc/Report_a_Bug

Regards,
Curtis


On Mon, Sep 10, 2012 at 6:49 AM, Ellen Batchelder <EBatchelder at unity.edu>wrote:

> 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.  ****
>
> ** **
>
> ** **
>
> *From:* Ellen Batchelder
> *Sent:* Monday, September 10, 2012 7:49 AM
> *To:* 'ctrueden at wisc.edu'
> *Cc:* Chaz James
> *Subject:* Request for help with file format****
>
> ** **
>
> Hi Chris,****
>
> 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… ****
>
> ** **
>
> 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.****
>
> 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 ?  ****
>
> ** **
>
> Any thoughts would be appreciated….****
>
> ** **
>
> Sincerely,****
>
> Ellen Batchelder****
>
> ** **
>
> ** **
>
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