Running GIANI Headlessly

Overview

If you wish to run GIANI in environments with no graphical capabilities (e.g.: HPC clusters), then you can use the “headless” mode, which allows you to run GIANI as a command line tool. In order to run GIANI in headless mode, you will need a properties.xml file. If you do not have a properties.xml file, one can be generated by using the graphical user interface in FIJI to specify the parameters for your analysis.

When running GIANI in headless mode, you must specify at least:

  • The location of a properties.xml file

  • One or more files to be processed.

For example, the following command will run GIANI on a file called test_image.ome.tiff file using properties.xml:

java -jar <Path to FIJI/plugins/giani*.jar> -f test_image.ome.tiff -p properties.xml

You need to replace <Path to FIJI/plugins/giani*.jar> with the full path to the giani*.jar in your FIJI plugins directory. The above command will look exactly the same, regardless of whether you are running GIANI on Windows, Linux or Mac.

Parameters

The full list of parameters that can be passed to GIANI is as follows:

  • -f: The full path to the image file you wish to analyse.

  • -p: The full path to the properties.xml file.

  • -s: If the input image file is a multi-series image dataset, then you need to specify which image series you wish to analyse. Otherwise, GIANI will just analyse the first image in the series.

  • -o: The directory where you wish outputs to be saved. If not specified, GIANI will create an output directory in the parent directory of the input file.

  • -h: Prints the link to this page and exits.

Deprecated parameters - will be removed in a future release:

  • -l: The pull path to a CSV file containing a list of image files you want GIANI to analyse (see below).

  • -n: If a list of files was provided above, this parameter tells GIANI which file in the list to analyse (see below).

Path to GIANI job list (Deprecated - will be removed in a future release)

The full path to a text file containing a list of all the images you wish to analyse with GIANI. The format of this file is very simple and should contain the following:

0, <Path to Image 1>, 0

1, <Path to Image 2>, 0

2, <Path to Image 3>, 0

3, <Path to Image 4>, 0

4, <Path to Image 5>, 0

5, <Path to Image 6>, 0

6, <Path to Image 7>, 0

7, <Path to Image 8>, 0

8, <Path to Image 9>, 0

9, <Path to Image 10>, 0

The first column specifies the job number, which can be specified by the -n parameter when running GIANI. The second column lists the images to be analysed. The final column specifies the series within the specified file that is to be analysed.