CloudScope v0.2.0

acqstore (backend / data model)

Added:

• ND2 (Nikon) file loader wired into the loader factory, registry, and supported import extensions.
• OME-Zarr load and export (ome_zarr_file_loader, acq_image.io.ome_zarr) via bioio/zarr.
• TIFF export helpers and AcqImage.save_as_tif / AcqImage.save_reference_as_tif.
• Sum-intensity (ΔF/F₀) analysis module: core detection, event features, detection presets, and a synthetic data generator.
• Heart-rate analysis and velocity-event analysis as first-class dependent analyses computed from a parent radon_velocity analysis.
• Self-populating analysis registry with a get_analysis_by_type lookup.
• AcqAnalysisSet.find_analysis(...) lookup helper.
• Analysis pools for collection-level summaries: sum-intensity, velocity, and a shared base analysis pool.
• Randomized manifest / master-sampling API (AcqImageManifest) for blinded review workflows.
• Registered downloadable sample datasets diameter-sample-data and velocity-sample-data via acqstore.sample_data.ensure_sample() (same keys as the GUI sample-data menu items).
• Image-header physical-unit metadata loaded from a sidecar on file open.
• Analysis run metadata (analysis_date, analysis_time, analysis_version) stamped into velocity, diameter, heart-rate, and event summaries via BaseAnalysis.finalize_summary().
• DiameterAnalysis.summary_columns schema for collection-level analysis pools.
• AcqTrace backend for electrophysiology-style traces, including an ABF (.abf) loader, sweep/epoch tables, sidecar JSON save, and trace peak-detection analysis.
• dff0_diameter_analysis common-analysis package for paired reporter + diameter coupling (continuous and triggered-event workflows).

Changed:

• OIR loader emits proper x/y axis labels; OIR and CZI folder-load performance improvements.
• OIR line-scan physical units from seriesInterval + pixel length; reference-image spatial scales from parent pixel length.
• CZI line-scan t→y dimension remap and reference-image dimension handling.
• Calibration / dimension-unit handling improvements for image headers and loaders.
• Structured load-error reporting (LoadErrorType) for missing files, unsupported types, loader errors, and CSV errors, including clearer failed-TIFF messages (e.g. Olympus 2-channel).
• Signal filtering can interpolate through small NaN gaps where applicable.

nicewidgets (reusable NiceGUI widgets)

Added:

• New Plotly-based plotly_plot widget (context menu, display options, event overlay, models), replacing the ECharts analysis plot.
• Interactive velocity-event create/edit/delete in plotly_plot via selection handling.
• Interactive Set F₀ / baseline editing support in Plotly plots (hline drag, constrained drag, percentile toolbar helpers).
• Reusable ContrastWidget (LUT select, Auto, and min/max range) embedded in the image toolbar.
• UploadWidget for browser file upload.
• Interactive ROI editing in the raster viewer (create / move / resize ROI overlays).
• tree_widget promoted into nicewidgets with an index column.
• NicePool plot presets (save/load/delete), pool control panel, selection handler, preset validation, and table metadata display.
• Compact select styles and compact image-toolbar UI.
• plotly_axis_layout / plotly_layout_margins helpers for aligned x-axes across stacked plots.
• NicePool.relayout_plots() for plot refresh after embedded resize.

Changed:

• Raster viewer migrated to Plotly: relayout-based zoom/pan, trace and ROI overlays, margin alignment with plotly_plot.
• NicePool single-scrollbar toolbar layout; embedded h-full / min-h-0 sizing instead of h-screen.

Fixed:

• Plotly user-set x-range infinite-loop (echo) fix.
• ROI rectangle edit flashing/padding in the raster viewer.
• File-tree selection / scroll-into-view reliability (initial selection, programmatic vs user click, reduced selection flash).

cloudscope (app / GUI)

Added:

• Sum-intensity analysis view, parameters view, plot view, and pool integration.
• Interactive Set F₀ mode in the sum-intensity plot (live baseline edit, dual-plot / toolbar controls).
• Right-side velocity pool panel on the home page: collapsible splitter, persisted open width, header toggle, and lazy build.
• Primary-image t/z slicing sliders with viewport preservation while scrubbing.
• Blinded display mode.
• App Info log viewer (Open Logs button + in-app log preview) backed by a unified cloudscope.log.
• Live build-info rows in App Info (version / build metadata when packaged or deployed).
• Batch-analysis dialog with ROI-mode selection, preview rows, live per-file results, progress, and cancellation.
• Split experiment-metadata and image-header metadata into distinct views with a dedicated left-toolbar button.
• Reference-image metadata display and Save Reference As Tif (native dialog + browser download).
• analysis_summary_display helpers for formatted velocity/diameter summary expansions.
• Factory reset in runtime and the options view.
• Reference-image scan-path traces; reference image relocated to the left toolbar.
• x-range controller, sum-intensity pool controller, and velocity pool controller.
• VelocityPoolView.relayout_plots(), SplitterManager right-pool helpers, and RIGHT_POOL splitter preset.

Changed:

• Home page layout refactor for natural scrolling and right-toolbar pool integration.
• Velocity and diameter analysis views show a collapsed summary expansion instead of a raw dict; summary floats rounded to three decimals.
• Velocity pool column naming no longer double-prefixed (velocity_velocity_mean → velocity_mean).
• App-config table font and dark-mode UI polish.
• File tree auto-fits to splitter height; load file/folder buttons disabled in web-server mode.
• Disconnect/reconnect session restore and page-layout chrome restore improvements.

Fixed:

• Reference image view when no reference image is present (clear on missing).
• Diameter analysis int→float mapping bug.
• Reference plot physical-axis display when calibration metadata is present.

acqstore_server

Added:

• New acqstore_server package: HTTP API over acqstore loaders (API-only uvicorn and optional native status UI).
• Session pick/open lifecycle, reference/overview payloads, and demo HTML clients (v1 and v2).
• v2 API surface: capabilities, session lifecycle, OpenAPI discoverability, stable error envelopes, and header contract.
• Gzip-friendly session fetch path for large payloads.
• Manual-dispatch macOS packaging workflow for AcqStore Server (separate from CloudScope desktop releases).

Desktop app

Added:

• Option C desktop quit flow with a native Save / Don't Save / Cancel dialog and synchronous dirty-file save on quit.
• Native window menu title.
• Desktop app icons (CS) for macOS and Windows packaging.

Changed:

• Desktop launcher defaults back to single-window mode; the velocity pool is embedded in the home page instead of a separate native window.
• WindowGeometryTracker syncs live geometry on window close before persisting config.
• Windows / macOS build scripts and CI path fixes; build-info embedded in packaged artifacts.

Fixed:

• Option C window geometry could be lost when closing because persistence ran after the pywebview window was destroyed.
• Embedded velocity pool plots could fail to relayout after the right-panel splitter was resized.

Documentation

• Major MkDocs restructure with expanded end-user recipes (velocity, diameter, sum-intensity, velocity-event, heart-rate).
• New notebooks: sum intensity, heart rate, heart-rate batch, kymograph reference image, and generating a randomized file subset for unbiased analysis.
• New blinded-mode and supported-file-formats end-user pages; a heart-rate data-scientist page; and heart-rate, event-analysis, and analysis-pool API pages.
• MkDocs notebooks transition from the retired demo-small sample to the registered diameter-sample-data and velocity-sample-data datasets.
• New install-desktop-app guide (form-based desktop distribution) and desktop-app request form; empty-__init__ and no-README-driveby contributor policies.
• Google Analytics on the MkDocs site (and web-server HTML injection for the hosted app).

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CloudScope v0.1.3

Added

• Two-window desktop mode: home page + plot pool in separate native windows.
• Desktop launcher with pywebview, window geometry persistence, and theme sync.
• Lazy TIFF loading in acqstore file loaders.
• CZI reference image support and dimension handling improvements.
• Load controller integration with task runner for file-tree loads.
• LRU cache for image pyramid builds; raster display cache in cloudscope.
• SmartExpansion in nicewidgets: when expansion is closed, child BaseView(s) disconnect from MVC for responsiveness; when open, they reconnect and refresh from current app state.
• SmartExpansion on home page for file list, analysis plot, and reference image panels.

Changed

• Refactored native windowing away from NiceGUI main_window to pywebview.
• Updated home page splitter to use SmartExpansion.
• Raster viewer: relayout-based zoom/pan, pyramid level constraints, kymograph fixes.
• acqstore scan-path / reference-image API updates.

Fixed

• macOS PyInstaller multiprocessing freeze (multiple window relaunch).
• Plotly mouse+wheel zoom and heatmap corruption with space dim 1.
• macOS two-finger context menu in Plotly raster view.
• Reference image view when no reference image is present.

Documentation

• Added kymograph reference-image MkDocs notebook.
• Expanded velocity, diameter, and heart rate notebooks.

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CloudScope v0.1.2

Fixed

• Fixed macOS build metadata generation when building from a git tag.

• Fixed the automated macOS release asset build path for tagged releases.

CloudScope v0.1.1

Added

• Implemented MkDocs documentation site using Material for MkDocs and mkdocstrings.

• Added expanded documentation structure for end users, scientific users, and developers.

• Added GitHub Actions workflows for building Windows and macOS desktop application artifacts.

• Added signed, notarized, and stapled macOS Apple Silicon application build workflow.

• Added unsigned Windows desktop application build workflow using NiceGUI Pack and PyInstaller.

Changed

• Added new ECharts context menu items.

• Improved CI/CD release process for reproducible tagged CloudScope releases.

• Improved desktop build artifact naming and packaging conventions.

Fixed

• Fixed release notes extraction for GitHub Release generation.

CloudScope v0.1.0

Added

• Added first official GitHub Release workflow for reproducible CloudScope releases.
• Added local release metadata checks for tag, version, and changelog consistency.
• Added docs and source archive artifacts to GitHub Releases.

Changed

• Improved GitHub Actions run names for easier reading in the Actions UI.