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ZedProfiler Roadmap

This file is for planning of new modules, features, and PRs that are needed the release(s) of ZedProfiler. The roadmap is organized into phases, with each phase containing a set of PRs that build upon each other. The roadmap is intended to be a living document and may be updated as needed.

Scope for current release

In scope

  • Handcrafted featurization modules:
    • volumesizeshape
    • Colocalization
    • Intensity
    • Granularity
    • Neighbors
    • Texture
  • Featurization helper utilities needed by the modules
  • Full test suite with coverage gate (>=85%)
  • Sphinx documentation
  • Example notebooks for module usage
  • Our RFC2119-specification driven feature naming policy

Architecture and Product Decisions

  • Linux-first, CPU-only, low RAM usage for the current release.
  • File-format agnostic APIs operating on NumPy arrays.
  • Input contracts:
    • Single-channel arrays: (z, y, x)
    • Multi-channel arrays: (c, z, y, x)
  • Modules are intentionally small and composable for external parallel orchestration.

PR Plan

Phase 1: Foundation (PR 1-3)

  1. PR 1: Packaging and environment baseline
  • Python package scaffold, uv dependency management, version metadata 0.0.1, lint/test tooling, CI skeleton.
  • Linux support and CPU-only scope statements in metadata and docs.
  1. PR 2: Core data model and API contracts
  • Canonical input contracts, loader interfaces, common error types.
  • Return schema contract (required keys, types, deterministic ordering).
  1. PR 3: RFC2119 naming specification and validators
  • Port and adapt naming conventions into this repository.
  • Add runtime and CI naming validation helpers and conformance tests.

Phase 2: Feature modules and tests (PR 4-9)

  1. PR 4: volumesizeshape module and tests

    • Implement module

  2. PR 5: Colocalization module and tests

    • Implement module

  3. PR 6: Intensity module and tests

    • Implement module

  4. PR 7: Granularity module and tests

    • Implement module

  5. PR 8: Neighbors module and tests

    • Implement module

  6. PR 9: Texture module and tests

    • Implement module

Phase 3: Integration, docs, release (PR 10-13)

  1. PR 10: Integration matrix and parallelization guidance
  • Cross-module integration tests and explicit non-goal docs for internal parallelization.
  1. PR 11: Example notebooks and public dataset references
  • One notebook per module plus one end-to-end chaining notebook.
  1. PR 12: Sphinx docs, logo, API docs
  • API pages, architecture and scope pages, docs build checks in CI.
  1. PR 13: Release v0.0.1 and publish workflow
  • Changelog, semantic tag, PyPI publish automation, README install updates.

Phase 4: Post-release improvements (PR 14+)

  1. Add the ability for loading of images from array instead of file file paths for increased flexibility in data sources and testing.

Verification Gates

  • Run full unit and integration tests on Linux with coverage >=85%.
  • Run naming validation tests for all emitted feature names.
  • Build Sphinx docs in CI with warnings treated as errors.
  • Execute example notebooks in a clean environment.
  • Validate install/import from both wheel and sdist.
  • Perform release dry-run before publishing.

v0.0.2 Backlog (Planned)

  • Nucleocentric featurization.
  • Optional mask output mode.
  • Expanded benchmark strategy.

v0.0.3 Backlog (Planned)

  • Potential Arrow Flight handoff experiments.