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

Displays a different series, for example the second one:

showinf -series 1 /path/to/file

Note that series numbers begin with 0.

-omexml

Displays 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

-option KEY VALUE

Passes options expressed as key/value pairs:

showinf -option key value /path/to/file

e.g. additional reader options, see Additional reader and writer options:

showinf -option leicalif.old_physical_size true /path/to/file

New in version 5.3.0.

-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 512×512 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

Displays the OME-XML alone:

showinf -omexml-only /path/to/file

This is particularly helpful when there are hundreds or thousands of series.

-debug

Enables debugging output if more information is needed:

showinf -debug /path/to/file

-fast

Displays an image as quickly as possible. This is achieved by converting the raw data into a 8 bit RGB image:

showinf -fast /path/to/file

Note

Due to the data conversion to a RGB image, using this option results in a loss of precision.

-autoscale

Adjusts the display range to the minimum and maximum pixel values:

showinf -autoscale /path/to/file

Note

This option automatically sets the -fast option and suffers from the same limitations.

-cache

Caches the reader under the same directory as the input file after initialization:

showinf -cache /path/to/file

-cache-dir DIR

Specifies the base directory under which the reader should be cached:

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

-format FORMAT

Specifies the reader to be used for opening the specified file. The utility will look for a reader named loci.formats.in.<FORMAT>Reader. If the reader does not exist or no -format option is passed, the file will be opened with loci.formats.in.ImageReader:

showinf -format APNG test.png