TrackRefiner can be executed in two different ways:

• Command-Line Interface (CLI): trackrefiner-cli

You can see the input parameters of Trackrefiner by using the following command:

trackrefiner-cli -h

• Graphical User Interface (GUI): trackrefiner-gui

Below are the parameters used in both the CLI and GUI, along with their corresponding GUI field labels:

• CLI Parameter: -i, --cp_output_csv
• GUI Label: CellProfiler Output CSV File

Path to the CellProfiler generated CSV file containing measured bacterial features (e.g., length, orientation) and tracking information.

Example: FilterObjects.csv

• CLI Parameter: -s, --segmentation_results
• GUI Label: Segmentation Results Folder

Path to a folder containing .npy files generated from segmentation by CellProfiler.

Example: objects.zip

• CLI Parameter: -n, --neighbor_csv
• GUI Label: Neighbor CSV File

Path to the CSV file containing bacterial neighbor information.

Example: Object relationships.csv

• CLI Parameter: -t, --interval_time
• GUI Label: Interval Time (minutes)

Time interval between frames, in minutes.

• CLI Parameter: -d, --doubling_time
• GUI Label: Doubling Time (minutes)

Minimum lifespan of bacteria, in minutes.

• CLI Parameter: -e, --elongation_rate_method
• GUI Label: Elongation Rate Method

Options:

• Average (default)
  • Calculates the average elongation rate of a bacterium over its lifecycle based on initial and final logarithm lengths
• Linear Regression
  • Calculates the elongation rate of a bacterium using linear regression on the logarithm of length as a function of time

Method to calculate elongation rate

• CLI Parameter: -p, --pixel_per_micron
• GUI Label: Pixel Per Micron

Conversion factor for pixels to micrometers. Default: 0.144.

• CLI Parameter: -a, --assign_cell_type
• GUI Label: Assign Cell Type

Enables or disables cell type assignment. Default: Enabled (checked).

• CLI Parameter: -c, --classifier
• GUI Label: Classifier

Options:

• LogisticRegression (default)
• C-Support Vector Classifier

Classifier for track refining

• CLI Parameter: -z, --num_cpus
• GUI Label: Number of CPUs

Number of CPUs for parallel processing. Default: -1 (all available CPUs).

• CLI Parameter: -b, --boundary_limits
• GUI Label: Boundary Limits

Define image boundaries to exclude objects outside the specified range. Format: Lower X, Upper X, Lower Y, Upper Y.

Example: 0,112,52,323 excludes objects outside X: 0–112 and Y: 52–323.

• CLI Parameter: -dy, --dynamic_boundaries
• GUI Label: Dynamic Boundaries

Specify a CSV file defining time-dependent boundary limits. Columns include:

• Time Step
• Lower X Limit
• Upper X Limit
• Lower Y Limit
• Upper Y Limit

Example: dynamic_boundaries.csv

• CLI Parameter: -dc, --disable_tracking_correction
• GUI Label: Disable Tracking Correction

Disables tracking correction on CellProfiler outputs and focuses only on calculating bacterial features. Default: Disabled (unchecked).

• CLI Parameter: -o, --output
• GUI Label: Output Folder

Folder to save results.

Default: Same folder as the CellProfiler output file.

• CLI Parameter: -v, --verbose
• GUI Label: Verbose Output

Enables detailed messages and warnings. Default: Disabled (unchecked).

• CLI Parameter: -k, --save_pickle
• GUI Label: Save in .pickle format

This option is useful for facilitating further analysis, as described in our study, "A Pipeline for Calibrating Agent-Based Models of Microbial Populations: From Image Collection to Model Parameterization" where input data for the scripts used in this paper or some packages must be provided in .pickle format.