Hi Oli,
> From a .lif file acquired with a Leica SP5 microscope (2 channels, 3 positions, 189 timepoints, 38 slices)
> When I want to open one of the positions, the resulting file contains parts of channel 2 at around the middle of the stack.
> If I extract the data from the software as a series of TIFF and open it in ImageJ, the ordering is good, so the problem does not come from the .lif file.
> This is an old dataset and I didn't have this problem when opening it with older versions of LOCI.
>
> This also happens with .lsm files. The trigger seems to be when there are a lot of slices in several dimensions.
It's not clear which version of Bio-Formats you are using currently, so
my first suggestion as usual is to try the latest trunk build and see
how that works.
If you see the same problem after updating, then it would be very helpful if
you could send at least one problematic dataset in each of the formats
mentioned, along with the options that you have selected when you open these
files in ImageJ. I think I have sent you our SFTP server information
previously, but can send it again privately if needed.
Regards,
-Melissa
On Thu, Apr 26, 2012 at 03:11:27PM +0000, Burri Olivier wrote:
> Dear all,
>
> I'm having problems with 5D image stacks in LOCI BioFormats.
>
> From a .lif file acquired with a Leica SP5 microscope (2 channels, 3 positions, 189 timepoints, 38 slices)
> When I want to open one of the positions, the resulting file contains parts of channel 2 at around the middle of the stack.
> If I extract the data from the software as a series of TIFF and open it in ImageJ, the ordering is good, so the problem does not come from the .lif file.
> This is an old dataset and I didn't have this problem when opening it with older versions of LOCI.
>
> This also happens with .lsm files. The trigger seems to be when there are a lot of slices in several dimensions.
>
> Thanks for any information!
>
> Best
>
> Oli
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