Note
This documentation is for the new Bio-Formats 5.1 version. See the latest Bio-Formats 5.0.x version or the previous versions page to find documentation for the version you are using.
The showinf command line tool can be used to show the images and metadata contained in a file.
If no options are specified, showinf displays a summary of available options.
To simply display images:
showinf /path/to/file
All of the images in the first ‘series’ (or 5 dimensional stack) will be opened and displayed in a simple image viewer. The number of series, image dimensions, and other basic metadata will be printed to the console.
To display a different series, for example the second one:
showinf -series 1 /path/to/file
Note that series numbers begin with 0.
To display the OME-XML metadata for a file on the console:
showinf -omexml /path/to/file
Image reading can be suppressed if only the metadata is needed:
showinf -nopix /path/to/file
A subset of images can also be opened instead of the entire stack, by specifying the start and end plane indices (inclusive):
showinf -range 0 0 /path/to/file
That opens only the first image in first series in the file.
For very large images, it may also be useful to open a small tile from the image instead of reading everything into memory. To open the upper-left-most 512x512 tile from the images:
showinf -crop 0,0,512,512 /path/to/file
The parameter to -crop is of the format x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image; x + width must be less than or equal to the image width and y + height must be less than or equal to the image height.
By default, showinf will check for a new version of Bio-Formats. This can take several seconds (especially on a slow internet connection); to save time, the update check can be disabled:
showinf -no-upgrade /path/to/file
Similarly, if OME-XML is displayed then it will automatically be validated. On slow or missing internet connections, this can take some time, and so can be disabled:
showinf -novalid /path/to/file
Most output can be suppressed:
showinf -nocore /path/to/file
and to display the OME-XML alone:
showinf -omexml-only /path/to/file
This is particularly helpful when there are hundreds or thousands of series.
Debugging output can also be enabled if more information is needed:
showinf -debug /path/to/file
Image display can be done as quickly as possible using:
showinf -fast /path/to/file
Note that this command results in a loss of precision.
In combination with the -fast option, the display range can be adjusted to the minimum and maximum pixel values:
showinf -fast -autoscale /path/to/file
After initialization, the reader can be cached under the same directory as the input file:
showinf -cache /path/to/file
It is also possible to specify the base directory under which the reader should be cached:
showinf -cache-dir /tmp/cachedir /path/to/file