Re: Problem opening Leica SP1 .lei file

Posted by ctrueden on Jun 20, 2008; 3:03pm
URL: http://imagej.273.s1.nabble.com/Problem-opening-Leica-SP1-lei-file-tp3695642p3695649.html

Hi Mike,

I would suggest giving Bio-Formats a try. The LEI reader in Bio-Formats
notices if any of the TIFF files have been renamed, tries to guess at what
happened, and sometimes even succeeds (though not always).

-Curtis

On Fri, Jun 20, 2008 at 3:49 PM, Michael Doube <[hidden email]>
wrote:

> Michael, Curtis
>
> I just used IJ in its 'natural' state, without the Bio-Formats plugin -
> actually very freshly installed straight from Wayne's website, no extra
> plugins added and running the jre from the ImageJ subdirectory.  It looked
> as though IJ was handling the .lei file but was stopped by a bug which meant
> it couldn't find the images that the .lei referred to.  I will see if I can
> get permission to send the files through to you Curtis.
>
> Mike
>
>
> Michael Weber wrote:
>
>> Mike,
>>
>> a very general answer, but: did you try the Bio-Formats plugin?
>>
>> Michael
>>
>>
>> Michael Doube wrote:
>>
>>> Hi all
>>>
>>> I tried to open someone else's images taken on a Leica SP1 confocal
>>> microscope by dragging and dropping the .lei file (which describes the
>>> imaging session) onto ImageJ, but I got an error that the directory couldn't
>>> be found - it looked as though the plugin was duplicating the directory name
>>> string then confusing itself by looking for ~/images/directory_1directory_1/
>>> instead of just ~/images/directory_1/
>>>
>>> I don't have access to the images right now so can't give exact details
>>> of the error message.  Can anyone else confirm this behaviour?
>>>
>>> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE.
>>>
>>> Mike
>>>
>>
> --
> Michael Doube  BPhil BVSc PhD MRCVS
> Research Associate
> Department of Bioengineering
> Imperial College London
> South Kensington Campus
> London  SW7 2AZ
> United Kingdom
>