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:
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.
Do not flatten resolutions into individual series:
showinf -noflat /path/to/file
Displays a different series, for example the second one:
showinf -series 1 /path/to/file
Note that series numbers begin with 0.
Displays 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
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.
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 512×512 tile from the images:
showinf -crop 0,0,512,512 /path/to/file
The parameter to
-cropis of the format
x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image;
x + widthmust be less than or equal to the image width and
y + heightmust 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
Displays the OME-XML alone:
showinf -omexml-only /path/to/file
This is particularly helpful when there are hundreds or thousands of series.
Enables debugging output if more information is needed:
showinf -debug /path/to/file
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
Due to the data conversion to a RGB image, using this option results in a loss of precision.
Adjusts the display range to the minimum and maximum pixel values:
showinf -autoscale /path/to/file
This option automatically sets the
-fastoption and suffers from the same limitations.
Caches the reader under the same directory as the input file after initialization:
showinf -cache /path/to/file
Specifies the base directory under which the reader should be cached:
showinf -cache-dir /tmp/cachedir /path/to/file
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
-formatoption is passed, the file will be opened with
showinf -format APNG test.png