The showinf
command line tool <index>
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.
showinf
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.
-noflat
Do not flatten resolutions into individual series:
showinf -noflat /path/to/file
-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 /formats/options
:
showinf -option leicalif.old_physical_size true /path/to/file
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
-novalid
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
-nocore
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
-swap DIMENSIONORDER
Overrides the default input dimension order:
showinf -swap XYZTC /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
-fill UNSIGNED_BYTE
Sets the fill value to use for undefined pixels. Valid values are 0-255, with 0 representing a black pixel and 255 representing a white pixel. The value set here will be applied to all bytes in an undefined pixel, e.g. setting to 128 (0x80) on a uint16 image will result in a pixel value of 32896 (0x8080). The default fill value is typically 0, but some readers may have different defaults.
6.13.0