Import of Leica LIF files

[kristiepy]

Dear ImageJ user,

I have taken some Z-stacks using Leica LAS and save all Z-stack series in one experiment file in LIF format. I have been trying to use LOCI plugin in ImageJ to access those files. I managed to import the first 20 Z-stacks series with no problem. However, when I tried to import the rest of it, there is an error saying "range out of bounds" and would not load up the Z-stack ivideo at all. All Z-stacks in the experiment were taken at 12-bits and their settings are exactly the same. One thing I did notice is that the thumbnail of those problematic Z-stacks did not show up in the window for importation selection, i.e. the window that displays the thumnail of all data series within the LIF file such that you can select those you need to importat. However, their file names were still displayed. So I am thinking those files they can still be identified???
I have installed the latest trunk build of LOCI and tried to restart the computer a few times to see whether it can be due to the lack of memory. Unfortunately, none of it helps.
Any idea to solve this problem will be very much appreciated

cheers
Kristie

[Melissa Linkert-2]

Hi Kristie,

Would you be willing to send the problematic LIF file to the
Bio-Formats developers so that we can see exactly where the problem
is?  I will send you the Bio-Formats FTP server information off-list,
in case you are interested in sending a file.

Regards,
-Melissa

On Thu, Jun 10, 2010 at 3:10 AM, kristiepy <[hidden email]> wrote:

> Dear ImageJ user,
>
> I have taken some Z-stacks using Leica LAS and save all Z-stack series in
> one experiment file in LIF format. I have been trying to use LOCI plugin in
> ImageJ to access those files. I managed to import the first 20 Z-stacks
> series with no problem. However, when I tried to import the rest of it,
> there is an error saying "range out of bounds" and would not load up the
> Z-stack ivideo at all. All Z-stacks in the experiment were taken at 12-bits
> and their settings are exactly the same. One thing I did notice is that the
> thumbnail of those problematic Z-stacks did not show up in the window for
> importation selection, i.e. the window that displays the thumnail of all
> data series within the LIF file such that you can select those you need to
> importat. However, their file names were still displayed. So I am thinking
> those files they can still be identified???
> I have installed the latest trunk build of LOCI and tried to restart the
> computer a few times to see whether it can be due to the lack of memory.
> Unfortunately, none of it helps.
> Any idea to solve this problem will be very much appreciated
>
> cheers
> Kristie
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Import-of-Leica-LIF-files-tp5162062p5162062.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[kristiepy]

Hi Melissa,
Thanks for your help.
I did show one of our technician the problem and she reckoned it was due to corrupted files.
I manage to retrieve the files again and they seem fine now.
cheers
Kristie

Melissa Linkert-2 [via ImageJ] wrote:

Hi Kristie,

Would you be willing to send the problematic LIF file to the
Bio-Formats developers so that we can see exactly where the problem
is?  I will send you the Bio-Formats FTP server information off-list,
in case you are interested in sending a file.

Regards,
-Melissa

On Thu, Jun 10, 2010 at 3:10 AM, kristiepy <[hidden email]> wrote:

> Dear ImageJ user,
>
> I have taken some Z-stacks using Leica LAS and save all Z-stack series in
> one experiment file in LIF format. I have been trying to use LOCI plugin in
> ImageJ to access those files. I managed to import the first 20 Z-stacks
> series with no problem. However, when I tried to import the rest of it,
> there is an error saying "range out of bounds" and would not load up the
> Z-stack ivideo at all. All Z-stacks in the experiment were taken at 12-bits
> and their settings are exactly the same. One thing I did notice is that the
> thumbnail of those problematic Z-stacks did not show up in the window for
> importation selection, i.e. the window that displays the thumnail of all
> data series within the LIF file such that you can select those you need to
> importat. However, their file names were still displayed. So I am thinking
> those files they can still be identified???
> I have installed the latest trunk build of LOCI and tried to restart the
> computer a few times to see whether it can be due to the lack of memory.
> Unfortunately, none of it helps.
> Any idea to solve this problem will be very much appreciated
>
> cheers
> Kristie
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Import-of-Leica-LIF-files-tp5162062p5162062.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

---

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