ActinTrackCV v1.1.1

ActinTrackCV v1.1.1

Researcher workflow improvements:

• Added Copy All Measurements to Measurement Inspector.
• Added CSV export for persisted individual measurements.
• Measurement exports retain persisted numerical precision rather than rounded display values.
• F-actin Orientation sample results are now explicitly identified as medians.
• Clarified that Condition Group Orientation values are means of capable sample medians.
• Corrected documentation to state that scientific timing uses the sample acquisition interval; video FPS remains playback metadata.

Scientific behavior:

• No scientific algorithms changed.
• No calibration formulas changed.
• No project or analysis-run schema migration is required.
• Existing v1.1.0 projects and analysis runs remain compatible.

Downloads

Platform	File
macOS Apple Silicon (arm64)	ActinTrackCV-1.1.1-macos-arm64.zip
Windows 10/11 x64	ActinTrackCV-1.1.1-windows-x64.zip

Both packages identify as application version 1.1.1 and were built from tag v1.1.1.

Windows (primary researcher package)

1. Download ActinTrackCV-1.1.1-windows-x64.zip.
2. Unzip it.
3. Open the ActinTrackCV folder.
4. Double-click ActinTrackCV.exe.
5. Keep the whole folder together — do not move ActinTrackCV.exe out on its own.

This Windows build is unsigned. Windows SmartScreen may warn on first launch: More info → Run anyway.

macOS (Apple Silicon)

1. Download ActinTrackCV-1.1.1-macos-arm64.zip.
2. Unzip it.
3. Open ActinTrackCV.app (first launch: right-click → Open, or System Settings → Privacy & Security → Open Anyway).

This macOS build is ad-hoc signed and not notarized. It is an Apple Silicon (arm64) package; Intel Macs are not claimed.

xattr -dr com.apple.quarantine /path/to/ActinTrackCV.app

Workspaces stay in the user’s Documents folder (ActinTrackCV), not inside the app.

ActinTrackCV v1.1.0

ActinTrackCV v1.1.0 expands the Workbench to support both video and static-image analysis and adds per-sample scientific calibration.

Downloads

Platform	File
macOS Apple Silicon (arm64)	ActinTrackCV-1.1.0-macos-arm64.zip
Windows 10/11 x64	ActinTrackCV-1.1.0-windows-x64.zip

Both packages identify as application version 1.1.0 and were built from tag v1.1.0.

Windows (primary researcher package)

1. Download ActinTrackCV-1.1.0-windows-x64.zip.
2. Unzip it.
3. Open the ActinTrackCV folder.
4. Double-click ActinTrackCV.exe.
5. Keep the whole folder together — do not move ActinTrackCV.exe out on its own.

This Windows build is unsigned. Windows SmartScreen may warn on first launch: More info → Run anyway.

macOS (Apple Silicon)

1. Download ActinTrackCV-1.1.0-macos-arm64.zip.
2. Unzip it.
3. Open ActinTrackCV.app (first launch: right-click → Open, or System Settings → Privacy & Security → Open Anyway).

This macOS build is ad-hoc signed and not notarized. It is an Apple Silicon (arm64) package; Intel Macs are not claimed.

xattr -dr com.apple.quarantine /path/to/ActinTrackCV.app

Workspaces stay in the user’s Documents folder (ActinTrackCV), not inside the app.

Highlights

• IMAGE support for JPG, JPEG, PNG, TIF, and TIFF
• F-actin Orientation analysis for supported image samples
• mixed VIDEO + IMAGE samples within the same Condition Group
• Toward Nucleus measurements
• Measurement Inspector / Show All Measurements
• numeric measurement-table sorting
• per-sample acquisition interval
• 30-second and 60-second acquisition presets
• per-sample spatial calibration in µm/pixel
• biological acquisition timing separated from video playback FPS
• improved CellRegion performance
• substantially faster IMAGE sample switching
• Explorer drag-and-drop improvements
• calibration provenance stored with analysis runs

Important scientific note

Video playback FPS is not used as biological acquisition timing. Researchers should enter the actual time between acquired frames and the appropriate spatial calibration for each sample.

Scientific velocity:

velocity_um_per_s = displacement_px * microns_per_pixel / acquisition_interval_s

Legacy compatibility fallbacks (only when a sample has no explicit calibration): 60 s/frame and 0.265 µm/pixel.

What this release does not claim

• Automatic scale-bar or microscopy-metadata calibration
• Equivalence with historical ImageJ arbitrary-unit measurements
• Signed or notarized macOS distribution
• A signed Windows executable
• 3D stack thickness/depth analysis

ActinTrackCV v1.0.0 (macOS + Windows)

First scientific Workbench cut for the Sapkota Lab. Unsigned builds — expect Gatekeeper (Mac) or SmartScreen (Windows) on first launch.

Downloads

Platform	File
macOS Apple Silicon	ActinTrackCV-1.0.0-macos-arm64.zip
Windows 10/11 x64	ActinTrackCV-1.0.0-windows-x64-onefolder.zip

Mac

Unzip → open ActinTrackCV.app. First launch: right-click → Open, or:

xattr -dr com.apple.quarantine /path/to/ActinTrackCV.app

Windows

Unzip → open the ActinTrackCV folder → double-click ActinTrackCV.exe. Keep the whole folder together (do not move only the .exe). SmartScreen: More info → Run anyway.

Workspaces stay in the user’s Documents folder (ActinTrackCV), not inside the app.

What this build includes

• Automatic Cell Boundary (full frame) plus a required Measurement Cutoff
• Optional Nucleus for Toward Nucleus and F-actin Orientation
• Detected video timing for µm/s (1 / observed_video_fps)
• Explicit Run Metrics — Metric Analysis inspects a saved run only
• Analysis compares General Movement, Optical Flow, Toward Nucleus, and F-actin Orientation

Notes

• Older v0.2.2 remains available.
• Plain-language packaging write-up: docs/PACKAGING_V1_REPORT.md on branch phase-v1-measurement-fidelity / PR #7.
• Merge #7 if you want this on main.

ActinTrackCV v0.2.2 for macOS

ActinTrackCV v0.2.2 for macOS

This release provides a macOS Apple Silicon build of ActinTrackCV. Windows remains available from the v0.2.1 release. Linux packages are not included.

macOS note:
This app is currently unsigned and not notarized. On first launch, macOS may block it. Use right-click → Open, or System Settings → Privacy & Security → Open Anyway.

Highlights:

• New Workbench/Explorer workflow polish.
• Condition Group and Sample hierarchy improvements.
• Explicit Run Metrics workflow.
• Selecting samples no longer schedules metric analysis automatically.
• Toolbar Run Metrics runs the currently displayed Sample.
• Explorer right-click Run Metrics can run:
  • one Sample,
  • selected Samples within one Condition Group,
  • an entire Condition Group.
• Batch-style Explorer metric runs are all-or-nothing when ROI/Region data is missing.
• Missing ROI/Region feedback is shown directly in the context menu.
• Empty Condition Groups behave visually like folders.
• Explorer expansion and selection state are preserved more reliably.
• Metric status wording is clearer: No Metrics, Stale, Analyzing, Analyzed.
• README documentation updated for the explicit metrics workflow.

Validation:

• Source tests passed: 361 tests.
• Fresh macOS frozen app was built from commit b527cf6.
• Manual validation passed for launch, import, ROI save/reload, Toolbar Run Metrics, Explorer Sample Run Metrics, selected-sample Run Metrics, Condition Group Run Metrics, output generation, Analysis view, and Help/README access.

Known limitations:

• The macOS app is unsigned and not notarized.
• Large selected-sample or Condition Group metric runs may block the UI while running.
• Background/async analysis workers and cancellation are planned for a future phase.
• The macOS build is Apple Silicon only.

ActinTrackCV 0.2.1

Windows-focused stabilization release. The macOS build remains at v0.2.0 (see that release for the macOS download).

Fixes & improvements

• Odd-dimension videos (odd width or height) are normalized to even dimensions on import using bundled FFmpeg, fixing the black/garbled frames seen in frozen Windows builds. Padding is top-left anchored, so ROI coordinates and microns-per-pixel stay valid. Even-dimension videos are copied byte-for-byte.
• Import failures no longer crash the app. Unreadable/unsupported videos and decode errors now surface a clear dialog and create no Sample.
• imageio-ffmpeg is bundled into frozen builds, and the build now fails fast if the dependency is missing.
• No more console flash — suppressed the FFmpeg console window that briefly appeared when importing MP4s on Windows.
• Added opt-in diagnostic logging (ACTINTRACKCV_DEBUG) and a console debug build option (ACTINTRACKCV_CONSOLE) for field troubleshooting.
• Hardened .gitignore for release/workspace hygiene.

Download (Windows 10/11 x64)

1. Download ActinTrackCV-0.2.1-windows-x64-onefolder.zip below.
2. Unzip it and open the ActinTrackCV folder.
3. Double-click ActinTrackCV.exe. Keep the whole folder together (the .exe needs the _internal folder next to it).

Unsigned pre-release build — Windows SmartScreen may warn on first launch (More info -> Run anyway). Workspace data defaults to Documents\ActinTrackCV.

Active import formats: AVI and MP4 only.

ActinTrackCV 0.2.0 — macOS & Windows pre-release

Unsigned pre-release for macOS (Apple Silicon) and Windows 10/11 x64 — intended for internal testing and early researcher validation. These are not signed, notarized, or polished installers. (Test samples are included but not required)

Install / open — macOS

1. Download ActinTrackCV-0.2.0-macos-arm64.zip below.
2. Unzip it (double-click in Finder).
3. Open ActinTrackCV.app.
4. Because the app is unsigned, macOS may block the first launch. If so, open System Settings → Privacy & Security, scroll to the message that "ActinTrackCV" was blocked, and click Open Anyway. After the first approval, it opens normally.

Install / open — Windows

1. Download ActinTrackCV-0.2.0-windows-x64.zip below.
2. Unzip it.
3. Open the ActinTrackCV folder and double-click ActinTrackCV.exe.
4. Keep the whole folder together — don't move ActinTrackCV.exe out on its own (it needs the _internal folder next to it).
5. Because the app is unsigned, Windows SmartScreen may warn on first launch — click More info → Run anyway.

Data & workspace

• Project/workspace data defaults to ~/Documents/ActinTrackCV (macOS) or Documents\ActinTrackCV under your user profile (Windows), created on first launch.
• Your external AVI/MP4 Data files stay outside the app — they are never bundled or deleted.

Known limitations

• Unsigned / not notarized on macOS (hence the Privacy & Security → Open Anyway step); unsigned on Windows (SmartScreen warning).
• ROI auto-suggestion sometimes fails and requires the user to manually press Suggest or define their own ROI.
• macOS build is Apple Silicon only — no Intel/universal build yet.
• No macOS .dmg and no Windows installer wizard yet (Windows ships as a one-folder zip).

ActinTrackCV v0.1.0 — Initial release (Template Tracking)

Release notes
ActinTrackCV v0.1.0
First public release of ActinTrackCV: a desktop app for ROI-level F-actin movement analysis in 2D Arabidopsis fluorescence time-lapse Data.

This release focuses on workspace organization, ROI definition, Template Tracking Motion Index, and read-only Analysis aggregation. Optical Flow is not included in this release.

Highlights
Breed → Sample → Data workflow — organize AVI/MP4 time-lapse files by experimental group and Sample
Orient and ROI — rotate/flip frames and draw a rectangular ROI around the actin-rich region; ROI autosaves as you work
Preview Cropped ROI — cropped playback with loop, frame scrubbing, and speeds from 0.25× to 2×
Template Tracking Motion Index — automatic draft tracking on cropped ROI frames using bright-feature template matching
Analysis view — read-only Breed/Sample summary from saved per-Sample results (does not re-run tracking)
Sample management — rename, replace Data, or delete Samples from the project tree
Template Tracking Motion Index
Runs on cropped ROI frames after orientation and crop.

Outputs (per Sample):

General Movement (µm/s)
Downward Motion (µm/s)
Configurable settings include starting points, minimum spacing, search radius, patch size, match confidence, lookahead frames, microns per pixel, and seconds per frame.

Draft results are saved under metadata/draft_tracking/ in the workspace.

Supported inputs
AVI and MP4 time-lapse Data only
Image sequences and 3D/raw microscopy formats are not supported in this release
Requirements
Python 3.10+
Dependencies: OpenCV, NumPy, pandas, PyQt6, tifffile (see requirements.txt)
Run:

python run_app.py
or ./run_app.sh (macOS/Linux) / run_app.bat (Windows)

Workspace layout
Local workspace folders (not part of the git repo):

raw/ — optional internal copies of imported Data
processed/ — cropped exports and motion-index outputs (when exported)
metadata/ — sample registry, ROI annotations, draft tracking results
Older workspaces are migrated automatically from legacy v1 metadata.

Known limitations
Metrics are draft ROI-level movement estimates, not individual filament tracking
Optical Flow Motion Index is planned for a future release
Results depend on consistent ROI placement and correct scale/time calibration (microns_per_pixel, seconds_per_frame)
Analysis reads saved results only; changing ROI or tracking settings requires re-entering Preview Cropped ROI to refresh draft metrics
Documentation
User guide: ActinTrackCV_User_Documentation_Refined.docx (in repo at this tag)