Running the analysis pipeline

You can run the analysis pipeline either via the command line interface (CLI) or using a script that incorporates the aliby.pipeline.Pipeline object.


On a CLI, you can use the aliby-run command. This command takes options as follows:

  • --host: Address of image-hosting server.

  • --username: Username to access image-hosting server.

  • --password: Password to access image-hosting server.

  • --expt_id: Number ID of experiment stored on host server.

  • --distributed: Number of distributed cores to use for segmentation and signal processing. If 0, there is no parallelisation.

  • --tps: Optional. Number of time points from the beginning of the experiment to use. If not specified, the pipeline processes all time points.

  • --directory: Optional. Parent directory to save the data files (HDF5) generated, ./data by default; the files will be stored in a child directory whose name is the name of the experiment.

  • --filter: Optional. List of positions to use for analysis. Alternatively, a regex (regular expression) or list of regexes to search for positions. Note: for the CLI, currently it is not able to take a list of strings as input.

  • --overwrite: Optional. Whether to overwrite an existing data directory. True by default.

  • --override_meta: Optional. Whether to overwrite an existing data directory. True by default.

Example usage:

aliby-run --expt_id EXPT_PATH --distributed 4 --tps None

And to run Omero servers, the basic arguments are shown:

aliby-run --expt_id XXX --host SERVER.ADDRESS --user USER --password PASSWORD 


Use the aliby.pipeline.Pipeline object and supply a dictionary, following the example below. The meaning of the parameters are the same as described in the CLI section above.

#!/usr/bin/env python3

from aliby.pipeline import Pipeline, PipelineParameters

# Specify experiment IDs
ids = [101, 102]

for i in ids:
        params = PipelineParameters.default(
            # Create dictionary to define pipeline parameters.
                "expt_id": i,
                "distributed": 6,
                "host": "INSERT ADDRESS HERE",
                "username": "INSERT USERNAME HERE",
                "password": "INSERT PASSWORD HERE",
                # Ensure data will be overwriten
                "override_meta": True,
                "overwrite": True,

        # Fine-grained control beyond general parameters:
        # change specific leaf in the extraction tree.
        # This example tells the pipeline to additionally compute the
        # nuc_est_conv quantity, which is a measure of the degree of
        # localisation of a signal in a cell.
        params = params.to_dict()
        leaf_to_change = params["extraction"]["tree"]["GFP"]["np_max"]

        # Regenerate PipelineParameters
        p = Pipeline(PipelineParameters.from_dict(params))

        # Run pipeline
    # Error handling
    except Exception as e:

This example code can be the contents of a file, and you can run it via


in the appropriate virtual environment.

Alternatively, the example code can be the contents of a cell in a jupyter notebook.