Command Line Interface (CLI)

The primary entrypoint for playNano is the playnano command-line tool. It provides interactive playback (GUI), batch processing/export, analysis runs, and an interactive wizard for building pipelines.

General usage

playnano <command> <input_file> [options]

Run playnano --help to see global options and a list of subcommands.

Available subcommands

  • play - Launch the interactive GUI viewer.

  • process - Batch mode: apply filters and export images/bundles/GIFs.

  • analyze - Run a pipeline of analysis modules (detection/tracking) on a stack and export results.

  • wizard - Interactive REPL for constructing processing/analysis pipelines.

  • env-info- Print environment information useful for debugging.

The CLI maps to the Python entry point playNano.cli.entrypoint:main.

Batch mode operations

Processing and analysis can be run in a non-interactive batch mode without a GUI or wizard.

Batch processing mode

Apply filters and export without user interaction.

playnano process /path/to/sample.h5-jpk \
  [--channel CHANNEL] \
  [--processing "remove_plane;row_median_align"] \
  [--processing-file pipeline.yaml] \
  [--export tif,npz,h5] \
  [--make-gif] \
  [--output-folder OUTPUT_DIR] \
  [--output-name BASE_NAME] \
  [--scale-bar-nm SCALE_BAR_INT] \
  [--zmin MINIMUM] \
  [--zmax MAXIMUM]

Primary options

  • --channel (default: height_trace) - channel name to load from the file.

  • --processing - semi-colon delimited inline pipeline string.

  • --processing-file - YAML/JSON file describing the processing pipeline.

  • --export - comma-separated list of formats to write: tif, npz, h5.

  • --make-gif - write an animated GIF with current annotations.

  • --output-folder / --output-name - export location and basename.

  • --scale-bar-nm - integer length (nm) for scale bar in GIF (0 disables).

  • --zmin / --zmax - initial z-range; can be a float or auto (1st/99th percentiles).

Note

--processing and --processing-file are mutually exclusive. Use one or the other (or neither to run with no processing).

Processing pipeline schema

Example pipeline YAML (see Processing for details):

filters:
  - name: remove_plane
  - name: gaussian_filter
    sigma: 2.0
  - name: threshold_mask
    threshold: 2
  - name: polynomial_flatten
    order: 2

Batch analysis mode

Run an analysis pipeline on an loaded AFM stack and export the results.

playnano analyze /path/to/processed_sample.h5 \
  [--channel CHANNEL] \
  (--analysis-steps "detect_particles:threshold=5;track_particles:max_distance=3.0" \
   | --analysis-file analysis.yaml) \
  [--output-folder OUTPUT_DIR] \
  [--output-name BASE_NAME]

Analysis options

  • --analysis-steps - semicolon-delimited inline steps (example below).

  • --analysis-file - YAML/JSON file specifying the analysis pipeline.

  • --output-folder / --output-name - export location and basename.

Inline example:

playnano analyze sample_flat.h5 \
  --analysis-steps "detect_particles:threshold=4.5;track_particles:max_distance=2.5" \
  --output-folder ./analysis_results --output-name run1

Analysis pipeline schema

Example YAML (see Analysis for full reference):

analysis:
  - name: detect_particles
    mask_fn: mask_threshold
    threshold: 5
  - name: track_particles
    max_distance: 3.0

Outputs

  • <output>.json - sanitized analysis record (suitable for downstream parsing).

  • <output>.h5 - full analysis bundle (if HDF5 export requested).

Wizard mode (interactive)

The wizard opens a small REPL to interactively build and run processing and analysis pipelines. Useful for experimentation and creating shareable YAML configurations.

playnano wizard /path/to/sample.h5-jpk --output-folder ./results --output-name demo

Common REPL commands

Processing pipeline commands

  • add <filter> - add a processing step (REPL prompts for parameters).

  • list - show the current processing pipeline steps.

  • save <path.yaml> - save the current processing pipeline as YAML.

  • run - execute the processing pipeline on the supplied input.

Analysis pipeline commands (prefixed with a)

  • aadd <analysis_step> - add an analysis step (REPL prompts for parameters).

  • alist - show the current analysis pipeline steps.

  • asave <path.yaml> - save the current analysis pipeline as YAML.

  • arun - run the analysis pipeline (runs any processing steps as configured if

    AFM stack contains only raw data).

Other utility commands

  • help - show available REPL commands.

  • quit - exit the wizard (this is a single, global quit that closes the entire session).

Play (GUI) mode

Open the PySide6 GUI viewer:

playnano play /path/to/sample.h5-jpk \
  [--channel CHANNEL] \
  [--processing "remove_plane;row_median_align"] \
  [--processing-file pipeline.yaml] \
  [--output-folder OUTPUT_DIR] \
  [--output-name BASE_NAME] \
  [--scale-bar-nm SCALE_BAR_INT] \
  [--zmin MINIMUM] \
  [--zmax MAXIMUM]

GUI highlights

  • Playback controls (play/pause, FPS slider, frame slider)

  • Toggle raw vs processed views and apply processing on demand

  • Z-scale histogram with draggable zmin/zmax lines and numeric spinboxes

  • Export panel: NPZ, OME-TIFF, HDF5 and GIF export options

  • Keyboard shortcuts: Space (play/pause), F (apply filters), R (toggle raw/processed), G (export GIF), E (export selected formats)

Notes about z-range

  • --zmin / --zmax accept a float or the string auto (default). When auto is used values are computed as the 1st and 99th percentiles of the stack.

env-info

Prints environment and dependency information to help debugging and issue reports:

playnano env-info

Help & usage

  • Subcommand help:

    playnano <subcommand> --help

    Example:

    playnano process --help

  • Global help:

    playnano --help

Tips & troubleshooting

  • If the CLI command is not found, ensure your environment is activated and that you installed the package (pip install -e .) in that environment.

  • If GIF export fails, check the input metadata (e.g. line_rate) and the console logs.

  • For Windows users, installing PySide6 via conda install -c conda-forge pyside6 can reduce platform-specific issues.