[ome-users] convert .lif file with bfconvert

Mark Hiner hiner at wisc.edu
Thu May 29 16:41:15 BST 2014

Hi Michael,

> The problem is that ./SCIFIOTestDriver itkSCIFIOImageIOTest
> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
> (and my little program) throws an exception.
> How do I use bfconvert the correct way for my case?

You used bfconvert correctly to convert your dataset. Just so it's clear,
if your goal was to produce an OME-TIFF:

> /SCIFIOTestDriver itkSCIFIOImageIOTest /path/to/output_series_0.ome.tiff

would be unnecessary, as you already have the OME-TIFF output from
bfconvert. The itkSCIFIOImageIOTest is an analogous tool to bfconvert
written in the Bio-Formats C++ framework. (although comparing the outputs
of the itkSCIFIOImageIOTest conversion would be a good way to check for
errors in the conversion process)

That said, I believe your conversion failed because the output was picked
up by the ITK TIFF ImageIO, which I believe only supports 3D data. The
itkSCIFIOImageIOTest utility does basically no automation - you have to
tell it exactly how to run, and because the SCIFIOImageIO is an external
module it is not prioritized by the ITK format detection framework over
internal modules (I'm not sure it's part of the automatic detection
framework at all, actually). So you need to force the use of the
SCIFIOImageIO for writing.

If you run:

 /SCIFIOTestDriver itkSCIFIOImageIOTest

with no arguments from the command line, it will print the usage +
available flags. The flag you wanted here is "-w"  to write with the
SCIFIOImageIO (which will use Bio-Formats, and thus the OME-TIFF writer).

So the final syntax is:

/SCIFIOTestDriver itkSCIFIOImageIOTest /path/to/output_series_0.ome.tiff
/path/to/scifiotest.ome.tiff -w

which worked for me locally.

Let me know if you have any other questions or issues!


On Thu, May 29, 2014 at 4:40 AM, Michael Meuli <michael.meuli at gmail.com>wrote:

> ./SCIFIOTestDriver itkSCIFIOImageIOTest
> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
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