[ImageJ-devel] [fiji-devel] slow opening of tif files using scifio-based ImgOpener

Curtis Rueden ctrueden at wisc.edu
Wed Feb 6 11:35:36 CST 2013

Hi all,

> Is there a way to turn this off?

Yes, you can call imageOpener.setAllowOpenFiles(false) which will prevent
Bio-Formats from doing any directory listings or opening up any files for
the purposes of determining the file format. However, if you set this flag,
some file formats will be improperly identified.

Out of curiosity: how much does the benchmark improve if that flag is set
inside ImgOpener's createReader method? Another thing you could test, to
determine the performance impact, is to change "new ImageReader" to "new
TiffReader", which explicitly tells ImgOpener to assume everything is a

If such changes vastly improve the ImgOpener performance, we could consider
adding another ImgOpener signature that lets you explicitly specify the
file format.

> Bio-formats analyzes the folder. Some formats are multi-file.

Indeed. And some files are even considered a different file format
depending on which other files are present in the same or nearby


P.S. to Melissa: Johannes has some ideas for improving the TIFF reader
performance too, which he plans to explore over the next few days. We will
keep you posted on any progress.

On Wed, Feb 6, 2013 at 11:13 AM, Albert Cardona <sapristi at gmail.com> wrote:

> 2013/2/6 Tobias Pietzsch <pietzsch at mpi-cbg.de>
>> Hi Melissa,
>> That is awesome! Thanks a lot for tackling these problems.
>> Out of curiosity, could you briefly explain (if there is an easy
>> explanation) why the 100.000-files-issue happens?
>> Is bioformats analyzing the directory the TIFF file lives in? Is there a
>> way to turn this off?
> Yes, Bio-formats analyzes the folder. Some formats are multi-file.
> Albert
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> http://www.ini.uzh.ch/~acardona/
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