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Release notes

Release notes describe behavior that changes when VIPP is upgraded. They are not a substitute for validating an analysis on representative and held-out data.

0.16.0a7 alpha

Read the 0.16.0a7 overview for initial source loading, recalculated automatic recovery results with manual/file-writing steps paused, and relative or absolute workflow-save paths. Scientific algorithms and schemas are unchanged; unfinished AI features are not included. Use the GitHub release and PyPI page.

0.16.0a6 alpha

Read the 0.16.0a6 overview for earlier responsive startup feedback, ordinary vector splash lettering, background reader preparation and bounded Windows setup retries. Scientific algorithms and schemas are unchanged. Use the GitHub release and PyPI page.

0.16.0a5 alpha

Read the 0.16.0a5 overview for standalone workflow crash recovery, portable workflow/batch/Python paths, no-overwrite image write protection, guided Windows GPU setup, registration-conflict guidance, graph routing and thumbnail cleanup. Unfinished AI assistant/agent/MCP/webhook features are not included. Use the canonical GitHub release and PyPI page with the matching installation instructions. Scientific algorithms, GPU admission and schema numbers are unchanged.

0.16.0a4 alpha

Read the 0.16.0a4 overview for linked image review with accepted live updates, bounded ImageJ Gaussian Blur and focused Batch/Results, window, threshold-control and OME compatibility fixes. Four review examples bring the catalogue to 35, with 34 bundled samples. Use the canonical GitHub release and PyPI page with the matching installation instructions. Review presentation does not change scientific arrays or add an AI, predictive tracking or GPU detection capability.

The OME-Zarr compatibility fix restores local 0.4/0.5 image and analysis-dataset exports with ome-zarr 0.20 and newer, retaining channel display metadata, calibration and VIPP history. It is not part of 0.16.0a3; format support does not imply complete metadata fidelity.

0.16.0a3 alpha

Read the 0.16.0a3 overview for fixed-template detection, calibrated basic tracking, read-only trajectory review and previous-frame registration. Four new examples bring the catalogue to 31. Node-card result shortcuts, practical slider windows and independent workflow-tab previews make review easier without changing scientific values. Use the canonical GitHub release and PyPI page with the matching installation instructions. This alpha adds no predictive or morphology-based tracking and no GPU detection/tracking operations.

0.16.0a2 alpha

Read the 0.16.0a2 overview for whole-volume registration and reusable transforms, same-grid image comparison, original-label skeleton measurements, exact CPU median acceleration and safer inspector scrolling. Four new examples bring the catalogue to 27. Use the canonical GitHub release and PyPI page with the matching installation instructions. Scientific, platform and exact-artifact qualification remain separate claims.

0.16.0a1 alpha

Read the 0.16.0a1 overview for the combined measurement, Results Workspace and seeded-segmentation features, suggested first examples, and compatibility limits. Use the canonical GitHub release and PyPI page with the matching installation instructions.

Changes after 0.15.0a5

  • Name graph nodes through the inspector's Name field or Rename…. Table Source, Statistics and Plot Results also receive descriptive automatic labels. Names stay consistent in the graph, Results Workspace, workflow search and connected-input descriptions, with source context and stable identifiers for matching names. Save, undo and copy names with the workflow; renaming leaves calculations and figure titles unchanged.
  • Results Workspace keeps Data, Summary and Plots beside their controls. Add or edit ordinary Statistics/Plot Results nodes with synchronized inspectors and windows, and explicitly choose original measurements or summary rows as the plot source. Table search and visible columns do not change the analysis or full-table exports. Maximize the window from its title bar, and use Workflow to choose any open workflow before browsing its data sources. Edits and calculations stay with the selected workflow. Decimal controls change table display precision without rounding stored measurements or exports; hover over a cell for its original value.
  • Plot axis spacing offers Auto or custom positive numeric tick intervals, with grid lines at those ticks and the same settings in exported figures. Count-axis intervals remain integers; category spacing and log axes use automatic ticks.
  • Statistics expands Summarize Measurements with descriptive object, image-mean and sample-mean summaries, explicit within-sample weighting, exclusion counts and retained units. New recipes report singleton sample SD as undefined; old summaries retain their previous behavior until explicit upgrade. No tests, p-values, significance labels or confidence intervals are added.
  • Plot measurement results as grouped points, histograms, cumulative distributions or scatter plots, with an editable window and sized raster/vector figure export. Distinguish objects from equally weighted image means; plots are descriptive.
  • Dialog buttons follow one platform-appropriate order: the main action then Cancel/Close on Windows, and the reverse pair on macOS. Stopping active work stays separate from dismissing its window; native file pickers are unchanged.
  • Collect batch measurements into one reviewed table and export CSV/TSV or Excel directly, without reprocessing images. Preserve image/object identities and annotations; retain empty and excluded images in the optional CSV/TSV image summary or the workbook's always-present Image summary sheet. Excel also includes Measurements and About this collection with units and run information. Saving a native VIPP dataset and opening it through Table Source are separate, optional steps. Collection itself does not calculate plots or statistical tests.
  • A separate three-dot Workflow actions menu after Save holds examples, Save workflow as… and exports, keeping them separate from the gear menu's settings. Saving and export behavior is unchanged.
  • Windows setup shows a live installation log for package downloads and installation. Scrolling up pauses automatic following; Jump to latest resumes it.
  • Six CellProfiler compartment profile nodes add the statistics paper's explicit 2D smoothing, thresholding, nuclear segmentation, seed preparation, cell-region finishing and cytoplasm construction. See the worked workflow and input and parameter reference. Agreement with the original CellProfiler runtime is recorded separately from reproduction of published measurements.
  • Grow Regions from Seeds — CellProfiler Propagation adds the 2D CPU Centrosome method with image, seed-label and Boolean mask inputs. It preserves seed IDs, requires one aligned YX plane and exposes regularization without hidden intensity normalization. See the task guide and compatibility boundary.
  • The seeded-segmentation guide also explains existing 3D watershed, including its voxel-grid distance and anisotropic-calibration limits.

0.15.0a5 alpha

  • 0.15.0a5 — guided examples, a Boolean colocalization mask and overlap-region counting, simpler desktop launch/update controls, and clearer inspector histograms and mesh-display warnings.

Use the canonical GitHub release and PyPI page. Use only the exact release assets and their matching checksum files.

0.15.0a5 writes workflow schema 6, batch config 6, and manifest schema 6. Valid supported earlier records retain explicit migration paths; recalculate and validate consequential results after upgrading.

Earlier releases

  • 0.15.0a4 — clearer graph-wire routing and overlapping multichannel histograms, including PNG/TIFF exports. Scientific calculations are unchanged from a3.

  • 0.15.0a3 — reviewed reproducibility packages, original-input checks, verified batch resume, object QC, broader RL GPU execution with advisories, and desktop/workflow presentation fixes.

  • 0.15.0a2 — included microscope readers and diagnostics, quiet update guidance, four threshold modes, explicit intensity inversion, safer controls, Convex Hull, and mesh-object creation/refinement/export.

  • 0.15.0a1 — task-based batch workflow, per-item output decisions, readable run reports, redesigned inspector and plots, reproducible intensity histograms, and hybrid mesh/skeleton measurement acceleration.

  • 0.14.0a3 — responsive volumetric Crop Stack, exact bounded local OME-Zarr reads for the sole-direct-Crop case, topology-safe bypass, improved save/undo behavior, and napari 0.9 compatibility.

  • 0.14.0a2 — native unsigned CPU-only macOS installers for Apple Silicon and Intel, detached-window resizing, cross-Qt compatibility, and a refreshed unsigned Windows installer. Its historical release page records the distinct GitHub and PyPI package hashes from that publication.

  • 0.14.0a1 — durable SourceItem identity, truthful microscope reader contracts, dynamic local OME-Zarr preview without changing analysis, typed per-sample batch values, restored Batch UX, and clearer installer capacity and activity.

The immutable a1 alpha is distributed on GitHub and PyPI. Its exact tag packages, intentionally unsigned installer, checksum, release manifest, and notices are available from the canonical GitHub release.

0.14.0a1 writes workflow schema 5 and batch config/manifest schema 4. Valid workflow schemas 3 and 4 and batch versions 1 through 3 retain explicit migration paths. Older records acquire SourceItems when sources are resolved; older batch records contain no per-sample parameter overrides. Workflow files do not contain cached results or source pixels. Recalculate and validate after upgrading, and regenerate Python exports because generated programs require the exact VIPP runtime version that created them.

  • 0.13.0a9 — Prefer GPU planning across CPU-only nodes, immediate QYX-to-ZYX inspector propagation, explicit volumetric skeletonization, stable sibling measurement caches, and actionable GPU VRAM preflight errors.

The immutable a9 alpha remains available on GitHub and PyPI. Its exact source, CI, focused GPU evidence, intentionally unsigned normal installer, and artifact hashes are recorded in the a9 release-verification table.

  • 0.13.0a8 — one standard CuPy-only GPU installation, CuPy background and basic-measurement providers, Remove Outliers, safer optimizer assignment, wire insertion, and explicit source-axis handling.

The immutable a8 alpha remains available on GitHub and PyPI. Its exact source, qualification boundary, installer, and artifact hashes are recorded in the a8 release-verification table.

  • 0.13.0a7 — visible one-click dtype repairs, readable per-implementation optimizer results, broader RL backend agreement, and a connected GPU segmentation/mask-cleanup example.

The immutable a7 alpha is public on GitHub and PyPI. Its exact source, CI, GPU admission, intentionally unsigned installer, seven release assets, hashes, and numbered-manual publication are recorded in the a7 release-verification table.

  • 0.13.0a6 — graph-fragment reuse and tunnel insertion, Compute Doctor 2.0, complete public-GPU admission checks, multi-series and Imaris sources, microscope metadata editing, and a public field checklist.

The immutable a6 alpha is public on GitHub and PyPI. Its exact source, CI, unsigned-installer status, artifact hashes, and numbered-manual publication remain recorded in 0.13.0a6 release verification.

  • 0.13.0a5 — checksum-first unsigned Windows setup, branded launchers, transactional install/update/repair, independently removable CPU and CUDA installations, and a separate optional cuCIM local-build bundle.

  • 0.13.0a4 — compatible NVIDIA CUDA 13 admission across GPU models meeting the released technical and scientific gates.

  • 0.13.0a1 — first evidence-gated GPU alpha with durable compute provenance, workflow tabs, and the schema-4 foundation.

  • 0.12.0a3 — direct batch execution, faster complete skips, more resilient provenance writes, suggested output destinations, and optional workflow-attached Batch workspace settings.

  • 0.12.0a2 — isolated node tuning, clearer actionable and waiting execution states, progressive previews, faster exact-pixel display, graph port-label controls, and more legible PSF/deconvolution guidance.

  • 0.12.0a1 — architectural and scientific-contract overhaul, workflow schema 3, deterministic batch provenance, retained representative navigation, and stricter source/grid validation.

VIPP is alpha software. Preserve the application version, workflow, inputs, environment, batch configuration, and manifests used for consequential work. Consult versions and compatibility before opening an older workflow in a newer release.