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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.

Displaying images and metadata

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.

-series SERIES

To display a different series, for example the second one:

showinf -series 1 /path/to/file

Note that series numbers begin with 0.

-omexml

To display the OME-XML metadata for a file on the console:

showinf -omexml /path/to/file
-nopix

Image reading can be suppressed if only the metadata is needed:

showinf -nopix /path/to/file
-range START END

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.

-crop X,Y,WIDTH,HEIGHT

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.

-no-upgrade

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
-no-valid

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
-no-core

Most output can be suppressed:

showinf -nocore /path/to/file
-omexml-only

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.

-debug

Debugging output can also be enabled if more information is needed:

showinf -debug /path/to/file
-fast

Image display can be done as quickly as possible using:

showinf -fast /path/to/file
-autoscale

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
-cache

After initialization, the reader can be cached under the same directory as the input file:

showinf -cache /path/to/file
-cache-dir DIR

It is also possible to specify the base directory under which the reader should be cached:

showinf -cache-dir /tmp/cachedir /path/to/file