[ome-users] czi multi-file images

[Melissa Linkert]

Hi Lorenz,

> as far as I can see from the code, when I have multi-file czis, every segment of every file is read by bioformats 4.4.10 already during initFile() of the main file.
> 
> I have 301 Files: the main metadata-only file “exp.czi”, and numbered data files “exp (1).czi”, “exp (2).czi”, …, “exp (300).czi” of 500 – 1000mb for each series.
> 
> If I would like to get only series 2 using the main file, the code will first read all 300 GB of data and then see that it needed only “exp (2).czi”. It finished after 6.5 hours. 
> 
> Opening any data file directly (except the first) throws an “IllegalArgumentException” that I mentioned here in an earlier mail. Back then I was told that this will not be fixed.
> 
> 
> That said, I tried to circumvent the problem by converting the .czi to tiffs beforehand. The Zeiss software created sub-directories called “exp (1)”, “exp (2)”…
> But the code doesn’t check if the numbered files are actually directories and throws an exception when trying to read them.

Have you tried your data with Bio-Formats 5.0.0-rc1?  There were several
improvements made to .czi support in 5.0.0-rc1 that were not part of
4.4.10.

If 5.0.0-rc1 doesn't provide better results, then it would be helpful if
you could send representative datasets that do not work as expected.
Smaller datasets can be uploaded to
http://qa.openmicroscopy.org.uk/qa/upload; if you have datasets larger
than 2 GB to send, please let me know and I will send alternate
instructions.

Regards,
-Melissa

On Tue, Feb 04, 2014 at 12:50:32PM +0100, Maier, Lorenz wrote:
> Dear all,
> 
> as far as I can see from the code, when I have multi-file czis, every segment of every file is read by bioformats 4.4.10 already during initFile() of the main file.
> 
> I have 301 Files: the main metadata-only file “exp.czi”, and numbered data files “exp (1).czi”, “exp (2).czi”, …, “exp (300).czi” of 500 – 1000mb for each series.
> 
> If I would like to get only series 2 using the main file, the code will first read all 300 GB of data and then see that it needed only “exp (2).czi”. It finished after 6.5 hours. 
> 
> Opening any data file directly (except the first) throws an “IllegalArgumentException” that I mentioned here in an earlier mail. Back then I was told that this will not be fixed.
> 
> 
> That said, I tried to circumvent the problem by converting the .czi to tiffs beforehand. The Zeiss software created sub-directories called “exp (1)”, “exp (2)”…
> But the code doesn’t check if the numbered files are actually directories and throws an exception when trying to read them.
> 
> Best,
> Lorenz
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users