[ome-users] czi multi-file images

Maier, Lorenz l.maier at dkfz-heidelberg.de
Tue Feb 4 11:50:32 GMT 2014

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.


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