Okay, sorry for the trouble: I poked around with imageJ a bit more, and did
file>import>raw to import the files, and this seemed to work, although the
images (two wavelengths) were interleaved. I was able then to separate out
the images with the image>stacks>tools>deinterleave command, which worked
perfectly, although I am not 100% sure whether all the images are exactly
where they are supposed to be, but they seem right. I wonder whether the
right metadata are there, and whether there were correction factors etc to
be applied before "wrapping up" in the usual .lsm format? Preliminary
analysis seems to look right anyway.
Thanks for those who replied, and sorry for the needless trouble, but maybe
someone else will be in this situation and will find my post...
All the best (and breathing a sigh of relief),
Jacob
On Thu, Jan 16, 2014 at 5:43 PM, John Hayes <
[hidden email]> wrote:
> Hi Jacob,
>
> I believe an .lsm file is just a special case of a .tif file (i.e., with
> more meta-data fields that are not-standardized).
>
> If you copy the .tmp file to another location with the extension .tif can
> you open it in ImageJ? If not, you might have to clean it up in a
> hexadecimal editor but that could be a mess depending on how the software
> writes things out (i.e., by full frame or by chunks of X-sized bytes).
>
> Or maybe someone else has a better suggestion because it’s not clear what
> file format you are using. I’ve used an LSM 510 in the past, and it had
> it’s own software that didn’t require ZEN 2009...
>
> HTH and best regards,
>
> John
>
> Le 16 janv. 2014 à 23:32, Jacob Keller a écrit :
>
> > Dear List,
> >
> > I recently collected a pretty long (~7000-frame) time-lapse dataset
> using a
> > 510 confocal and the software ZEN 2009, which upon finishing the
> successful
> > marathon data collection promptly crashed/froze. It seems that some files
> > were written, however, called .tmp files, but I have no idea of their
> > format nor whether it is possible to recover the dataset through these.
> > Googling does not turn up anything, so I thought maybe somebody here
> would
> > know. Does anybody know how to read these files, and/or whether they
> > contain the dataset? Can imageJ do the requisite reading/recovery?
> >
> >
> >
> > All the best,
> >
> >
> >
> > Jacob Keller
> >
> >
> >
> > *******************************************
> >
> > Jacob Pearson Keller, PhD
> >
> > Looger Lab/HHMI Janelia Farms Research Campus
> >
> > 19700 Helix Dr, Ashburn, VA 20147
> >
> > email:
[hidden email]
> >
> > *******************************************
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email:
[hidden email]
*******************************************
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