# What's New in *playNano* 0.3.0

**Release date:** 2026-03-06

This release extends the plugin system, adds new parameters to particle tracking and feature
detection, and introduces three breaking changes to output field names and data structures.

## Added

- **3D Stack Plugins:** The processing pipeline now supports 3D stack operations via a new
  `playnano.video_processing` entry point, alongside the existing `playnano.filters` entry
  point for 2D frame plugins. The CLI and interactive wizard recognise and expose video plugins
  as a step type.
- **Morphological Opening in Feature Detection:** `FeatureDetectionModule` now accepts
  `morph_opening` and `sep_radius` parameters to optionally separate touching or overlapping
  particles using per-object morphological opening with a configurable disk structuring element.
- **Gap-Tolerant Particle Tracking:** `ParticleTrackingModule` now accepts two new parameters:
  - `max_missing` — allows tracks to persist across frames with missing detections (default: 0,
    preserving previous behaviour).
  - `distance_scale` — scales the distance threshold with time since last detection using
    `"constant"` (default), `"linear"`, or `"sqrt"` modes.
- **Crop Padding:** `intersection_crop` and `crop_square` now accept a `pad` parameter to
  expand the crop region outward beyond the finite-pixel intersection, filling new pixels with NaN.
- **CI Improvements:** Pre-commit and test workflows now trigger on `dev` branch pull requests.
  The test workflow also supports `workflow_dispatch` for manual triggering.
- **CONTRIBUTING.md** covering development setup, project structure, code style, type hint and
  docstring requirements, branching workflow, and plugin contribution guidance.

## Changed

### Breaking Changes

- **Particle Tracking output structure:**
  - Track key `centroids` renamed to `coords`.
  - Tracks now use a dense representation spanning from first to last detection. Frames
    where a particle was not detected have `None` entries in `coords` and `point_indices`.
  - Migration: replace `track["centroids"]` with `track["coords"]` and handle `None` entries
    where `max_missing > 0`.

- **`flatten_particle_features` output columns:**
  - `mean_intensity`, `min_intensity`, `max_intensity` renamed to `mean`, `min`, `max`.
  - Migration: update any downstream code or saved pipelines referencing the old column names.

- **`intersection_crop` and `crop_square` metadata:**
  - `bounds` key replaced by `intersection_bounds` (exclusive-end coordinates).
  - New keys added: `intersection_shape`, `requested_bounds`, `applied_pad`, `pad_param`.
  - Migration: replace `meta["bounds"]` with `meta["intersection_bounds"]`.

- Pre-commit Python version pinned to 3.11; demo notebook kernels updated to 3.11.
- `markdownlint-cli2` downgraded to v0.10.0 as a workaround for a CI dependency conflict.
- Author name updated to "Daniel E. Rollins" in `pyproject.toml`.

## Fixed

- Numerous typos corrected across docstrings, inline comments, docs, and tests.
- CLI `SKIP_PARAM_NAMES` expanded to prevent internal array parameter names (`imarray`,
  `array`, `frame`, `video`) from appearing in the interactive wizard.

## Documentation

- API reference restructured with captioned sections: Core, Analysis, Analysis Modules,
  Processing, IO, CLI, and GUI.
- Module-level docstrings improved for `feature_detection` and `particle_tracking`,
  including `See Also` cross-references, version directives, and AI transparency notes.
- `processing.rst` updated to document the `playnano.video_processing` plugin entry point
  and link to the plugins repository.
- Various improvements to quickstart, processing, and notebook documentation pages.

## Pytest Coverage Added

- Morphological opening: single blob preservation, two-blob splitting, small blob fallback,
  label contiguity, dtype and shape checks.
- Particle tracking: gap tolerance, distance scaling modes, detection module fallback logic,
  missing coord and mask key handling.
- Video plugin resolution and step type identification.
- Crop padding: `_normalize_pad` valid and invalid inputs, `_crop_with_pad` in- and
  out-of-bounds behaviour, `intersection_crop` and `crop_square` with and without padding.
- `AFMImageStack.apply()` branches: video filter, video plugin, stack edit, method, and
  unrecognised step type.