[ome-users] NumberFormatException when importing image series using LOCI in ImageJ

[Roger Leigh]

On 12/03/2013 01:48, Dan Ruderman wrote:

> I am running into this Exception when importing an image sequence using
> the LOCI plugin.
>
> Error message:
>
> java.lang.NumberFormatException: For input string: "3t"
>      at
> java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
>
>      at java.lang.Integer.parseInt(Integer.java:458)
>      at java.lang.Integer.parseInt(Integer.java:499)
>      at loci.formats.in.CellomicsReader.initFile(CellomicsReader.java:292)
[...]
> These are some example Cellomics file names that I am importing.
>
> NRT4517CX-CLIEN_130306150005i3t001A01f17d1.C01
> through
> NRT4517CX-CLIEN_130306150005i3t060A01f17d1.C01
>
> 60 files total
>
>
> It seems like the expected file name format is not what is actually
> there (e.g.
> with the '3t' in it).  If anyone can clue me in to the correct filename
> format
> I would be very appreciative.

Dear Dan,

A quick look at the reader suggests that we might not currently parse
this part of the filename.  The same might also apply to the "i" and "d"
parts.

Please could you provide a sample (complete) Cellomics dataset which
fails to import, so that we can investigate this further?  It would also
be useful to know the exact dimensionality of the dataset so that we can
be sure what the metadata should look like.  You can upload a zip file
of the dataset here:
   http://qa.openmicroscopy.org.uk/qa/upload/

If you have any problems using the above, please let us know, and we can
try an alternative method.


Many thanks,
Roger Leigh

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096