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Command-line Interface

One asset of Cellogram is the possibility to process large amounts of data in automatically in a batch process. For this the command-line interface needs to be used. The command-line interface options are visible in Table 1.

Short Option Long Option Type Description
-h --help Print help message and exit
-i --input TEXT Input image.
-s --settings TEXT Path to json settings
-f --file TEXT Path to saved data for scene
-b --begin INT From which phase to run the script
-e --end INT Until which phase to run the script
-c --cmd Run without GUI

Table 1. Command-line interface options


  • -i --input This input is followed by a path to the image that is analyzed. For a batch process, iterate over different images

  • -s --settings This input determines the path to a json file that contains non-default parameters for Cellogram. The easiest way to generate this, is by running one image with the UI and saving a json of the data, which will include the settings.

  • -c Add this flag to not show the UI. This flag is required to do automatic processing. If it omitted, then Cellogram will only load the input file and the settings, but not do any processing.

  • -f --file If there is already data available, with which the batch process should start, then the path to this file is given with this argument. Be sure to adjust -b to not start from the first stage.

  • -b --begin Followed by an integer. See below which integer to choose:

    • 0: Fresh start
    • 1: Start with detection
    • 2: Start with reference position estimation
    • 3: Start with FEA

  • -e --end Followed by an integer. See below which integer to choose:

    • 1: End after detection
    • 2: End after reference position estimation
    • 3: End after FEA

Examples

  • Start Cellogram with image and settings 

    ./Cellogram.exe -i ./TestImages/QDs/1.tif -s ./TestImages/QDs/1/settings.json

  • Start Cellogram and run full analysis with default settings 

    ./Cellogram.exe -i ./test.tif -c

  • Start Cellogram and run full analysis with custom settings 

    ./Cellogram.exe -i ./test.tif -s ./settings.json -c

  • Start Cellogram and run FEA only with custom settings and loading available data 

    ./Cellogram.exe -i ./test.tif -s ./settings.json -f ./test/all.json -b 3 -e 3 -c