<commit_before>Troubleshooting
===============

This page is aimed at anyone who is responsible for supporting
Bio-Formats, but may also be useful for advanced users looking to
troubleshoot their own problems. Eventually, it might be best to move
some of this to the FAQ or other documentation.

General tips
------------

-  Make sure to read the
   `FAQ <http://www.openmicroscopy.org/site/support/faq>`_, particularly
   the "File Formats", "Bio-Formats", and "OME-XML & OME-TIFF" sections
-  If this page doesn't help, it is worth quickly checking the following
   places where questions are commonly asked and/or bugs are reported:

   -  `OME Trac <http://trac.openmicroscopy.org.uk/ome>`_
   -  `Fiji Bugzilla (for ImageJ/Fiji
      issues) <http://fiji.sc/cgi-bin/bugzilla/index.cgi>`_
   -  `ome-devel mailing
      list <http://lists.openmicroscopy.org.uk/pipermail/ome-devel>`_
      (not searchable)
   -  `ome-users mailing
      list <http://lists.openmicroscopy.org.uk/pipermail/ome-users>`_
      (not searchable)
   -  `ImageJ mailing list (for ImageJ/Fiji
      issues) <http://imagej.1557.n6.nabble.com/>`_

-  Make sure to ask for a \_specific\_ error message or description of
   the unexpected behavior, if one is not provided ("it does not work"
   is obviously not adequate).
-  "My (12, 14, 16)-bit images look all black when I open them" is a
   common issue. In ImageJ/Fiji, this is almost always fixable by
   checking the "Autoscale" option; with the command line tools, the
   "-autoscale -fast" options should work. The problem is typically that
   the pixel values are very, very small relative to the maximum
   possible pixel value (4095, 16383, and 65535, respectively), so when
   displayed the pixels are effectively black.
-  If the file is very, very small (4096 bytes) and any exception is
   generated when reading the file, then make sure it is not a `Mac OS
   X resource
   fork <http://en.wikipedia.org/wiki/Resource_fork#The_Macintosh_file_system>`_.
   The 'file' command should tell you:

   ::

       $ file /path/to/suspicious-file
       suspicious-file: AppleDouble encoded Macintosh file

Tips for ImageJ/Fiji
--------------------

-  The Bio-Formats version being used can be found by selecting "Help >
   About Plugins > LOCI Plugins".
-  "How do I make the options window go away?" is a common question.
   There are a few ways to do this:

   -  To disable the options window only for files in a specific format,
      select "Plugins > LOCI > LOCI Plugins Configuration", then pick
      the format from the list and make sure the "Windowless" option is
      checked.
   -  To avoid the options window entirely, use the "Plugins > LOCI >
      Bio-Formats Windowless Importer" menu item to import files.
   -  Open files by calling the Bio-Formats importer plugin from a
      macro.

-  A not uncommon cause of problems is that the user has multiple copies
   of loci\_tools.jar in their ImageJ plugins folder, or has a copy of
   loci\_tools.jar and a copy of bio-formats.jar. It is often difficult
   to determine for sure that this is the problem - the only error
   message that pretty much guarantees it is a "NoSuchMethodException?".
   If the user maintains that they downloaded the latest version and
   whatever error message/odd behavior they are seeing looks like it was
   fixed already, then it is worth suggesting that they remove all
   copies of loci\_tools.jar and download a fresh version.<commit_msg>Remove one more rogue "?"<commit_after>Troubleshooting
===============

This page is aimed at anyone who is responsible for supporting
Bio-Formats, but may also be useful for advanced users looking to
troubleshoot their own problems. Eventually, it might be best to move
some of this to the FAQ or other documentation.

General tips
------------

-  Make sure to read the
   `FAQ <http://www.openmicroscopy.org/site/support/faq>`_, particularly
   the "File Formats", "Bio-Formats", and "OME-XML & OME-TIFF" sections
-  If this page doesn't help, it is worth quickly checking the following
   places where questions are commonly asked and/or bugs are reported:

   -  `OME Trac <http://trac.openmicroscopy.org.uk/ome>`_
   -  `Fiji Bugzilla (for ImageJ/Fiji
      issues) <http://fiji.sc/cgi-bin/bugzilla/index.cgi>`_
   -  `ome-devel mailing
      list <http://lists.openmicroscopy.org.uk/pipermail/ome-devel>`_
      (not searchable)
   -  `ome-users mailing
      list <http://lists.openmicroscopy.org.uk/pipermail/ome-users>`_
      (not searchable)
   -  `ImageJ mailing list (for ImageJ/Fiji
      issues) <http://imagej.1557.n6.nabble.com/>`_

-  Make sure to ask for a \_specific\_ error message or description of
   the unexpected behavior, if one is not provided ("it does not work"
   is obviously not adequate).
-  "My (12, 14, 16)-bit images look all black when I open them" is a
   common issue. In ImageJ/Fiji, this is almost always fixable by
   checking the "Autoscale" option; with the command line tools, the
   "-autoscale -fast" options should work. The problem is typically that
   the pixel values are very, very small relative to the maximum
   possible pixel value (4095, 16383, and 65535, respectively), so when
   displayed the pixels are effectively black.
-  If the file is very, very small (4096 bytes) and any exception is
   generated when reading the file, then make sure it is not a `Mac OS
   X resource
   fork <http://en.wikipedia.org/wiki/Resource_fork#The_Macintosh_file_system>`_.
   The 'file' command should tell you:

   ::

       $ file /path/to/suspicious-file
       suspicious-file: AppleDouble encoded Macintosh file

Tips for ImageJ/Fiji
--------------------

-  The Bio-Formats version being used can be found by selecting "Help >
   About Plugins > LOCI Plugins".
-  "How do I make the options window go away?" is a common question.
   There are a few ways to do this:

   -  To disable the options window only for files in a specific format,
      select "Plugins > LOCI > LOCI Plugins Configuration", then pick
      the format from the list and make sure the "Windowless" option is
      checked.
   -  To avoid the options window entirely, use the "Plugins > LOCI >
      Bio-Formats Windowless Importer" menu item to import files.
   -  Open files by calling the Bio-Formats importer plugin from a
      macro.

-  A not uncommon cause of problems is that the user has multiple copies
   of loci\_tools.jar in their ImageJ plugins folder, or has a copy of
   loci\_tools.jar and a copy of bio-formats.jar. It is often difficult
   to determine for sure that this is the problem - the only error
   message that pretty much guarantees it is a "NoSuchMethodException".
   If the user maintains that they downloaded the latest version and
   whatever error message/odd behavior they are seeing looks like it was
   fixed already, then it is worth suggesting that they remove all
   copies of loci\_tools.jar and download a fresh version.
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