Quickstart

This short quickstart gets playNano running quickly (recommended: conda) using the CLI and GUI. For full details see the linked pages (Installation, Command Line Interface (CLI), GUI: Interactive Playback, Processing, Analysis).

2. Install playNano from PyPi

Install the latest release of playNano from PyPi using pip.

pip install playnano

3. Quick verification

playnano --help
python -c "import playnano; print(playnano.__version__)"

4. Most common actions (one-liners)

Launch interactive GUI:

To open a sample file in the GUI, run:

playnano play ./tests/resources/sample_0.h5-jpk  # Opens GUI with loaded file

This opens a sample AFM file when run in the project root. Change the path to your own data to view other files. There is a preset processing pipeline can can be applied by pressing the “F” key or the “Apply Filters” button in the GUI. You can find out more about using the GUI in GUI: Interactive Playback.

Batch process, analyis and export (no GUI):

For batch processing and analysis the processing and analyis pipelines are run through seperate commands. To run these commands on example data, these commands can be run from the project root.

playnano process ./tests/resources/sample_0.h5-jpk\
  --processing "remove_plane;mask_mean_offset:factor=1;row_median_align;polynomial_flatten:order=2" \
  --export h5,tif,npz --make-gif --output-folder ./results --output-name sample_processed

This will load demo data, apply a processing pipeline, export the processed data as an HDF5 file (h5), a NumPy zipped archive (npz) and a multi-page OME-TIFF (tif) to the ./results folder. It will also generate an animated GIF (from --make-gif) with scale bar and frame timestamp annotations.

Note

_filtered is automatically appended to the output name when processing is applied.

Run analysis (detection + tracking):

playnano analyze ./results/sample_processed_filtered.h5 \
  --analysis-steps "feature_detection:mask_fn=mask_mean_offset,factor=0.5,threshold=5;particle_tracking:max_distance=3"

5. Where to go next