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YOFO Review

YOFO Review is the Review tab as its own app for macOS and Windows. It opens the .h5 / .hdf5 files MIB Studio records, on any computer: no camera, hardware or MIB Studio installation is needed. Use it to browse a run, check masks and charts, export metrics and images, and regenerate masks after the experiment.

Install

Download the installer for your computer from the project's GitHub Releases page. YOFO Review releases are named YOFO Review X.Y.Z:

Computer File
Mac with Apple silicon, macOS 13 or later YOFO_Review_v<version>_aarch64.dmg
Windows 10 / 11, 64-bit YOFO_Review_v<version>_x64-setup.exe

Each release also lists SHA-256 checksums (SHA256SUMS-yofo-review.txt) so you can confirm the download.

macOS — open the DMG and drag YOFO Review into Applications. The app is not notarised by Apple, so the first launch is blocked. Open System Settings ▸ Privacy & Security, scroll to the message about YOFO Review and click Open Anyway. Later launches open normally.

Windows — run the setup program. It installs for your user account only and needs no administrator rights. The installer is not signed, so SmartScreen may warn: click More info ▸ Run anyway.

Open a file

  • Double-click a .h5 / .hdf5 file (the installer registers YOFO Review for both), or drag it onto the app icon.
  • Or use File ▸ Open… inside the app.

Opening another file replaces the current one. Close File on the toolbar (or File ▸ Close) releases the file, so you can move or delete it.

Files larger than 2 GB are fine: frames load as you browse. Recordings made in raw recording mode have no masks or metrics. For those, YOFO Review shows a single frame list, and only raw image export is available.

Browse frames and charts

Browsing works as in MIB Studio's Review tab (see Review & post-process):

  • Frames — thumbnails, the metrics table and the frame viewer, with mask, contour and ROI overlays. Double-click a thumbnail or a table row to open the viewer, then use ←/→ to step through frames.
  • Charts — the deformability-vs-area scatter and the ring-width histogram. Click a point to show that cell, scroll to zoom and drag to pan. Right-click for Reset zoom and Compute core contour from full run.

The status bar shows the file, its frame accounting, and the pixel-to-micron factor in use.

Export

The toolbar has Export Metrics to CSV… and Export All…. More… holds Batch Metrics, Batch Export All, Export Charts and Regenerate masks.

  • Export Metrics to CSV… writes <file>_metrics.csv. Existing files are never overwritten: a _2, _3, … suffix is added instead.
  • Export All… writes a folder named after the file, containing metrics.csv, the frame TIFFs and the chart images. For multi-image series it first asks whether to export all series frames, a range (for example 9-15), or none.
  • Batch Metrics / Batch Export All process several files in one go. The batch continues past a failed file and reports a summary at the end. Raw recordings have no metrics, so Batch Metrics lists them as failed.
  • Export Charts writes scatter_plot.tiff and ring_width_histogram.tiff (1200 × 1200) into a folder you choose. Exported charts always show the whole run, without zoom or the selection ring.

Every export runs behind a progress dialog with Cancel. A cancelled export leaves nothing behind. When an export finishes, Show in folder opens the output. Only one export runs at a time, and the app remembers the last output folder.

Regenerate masks

More… ▸ Regenerate masks runs mask processing again over the open file (all of it or a frame range), an AVI, or a folder of images. The result is a new HDF5 file, which opens when it is done; the original is never changed.

For HDF5 files, YOFO Review uses the processing settings, ROI and background the file was recorded with. Untick that option to use the default settings instead. AVI and image-folder sources always use the defaults.

Pixel-to-micron factor

Files record the pixel-to-micron factor they were taken with, and YOFO Review always uses it, for metrics, charts and exports (batches included). Older files that recorded no factor use the fallback set under File ▸ Preferences… (default 0.4886 µm per pixel); the status bar then marks the factor "(fallback)".

Updates

YOFO Review checks for a new version once at launch, and the status bar says when one is available. Help ▸ Check for updates… checks on demand and offers Install and restart.

Before installing, the app verifies that the update was signed by the YOFO Review release key and that its checksum matches the published one. If either check fails, nothing is installed.

Under File ▸ Preferences…, pick the update channel: stable (the default) or beta (pre-release builds, for testing).

Differences from MIB Studio's Review tab

YOFO Review was checked against the Review tab on recorded runs: metrics CSVs, exported images, chart axes and histogram bins, and saved core contours match. The visible differences:

  • The ring-width histogram spans the ring-ratio limits the file was recorded with (MIB Studio uses the current settings).
  • Batch Export All writes metrics and images for each file, but no chart images.
  • In a batch, the series question is asked once for all files.
  • Regenerate masks uses the file's recorded settings by default (see above).
  • Chart colours and legend order differ slightly.

Troubleshooting

  • "YOFO Review can't be opened" / "Apple could not verify…" (macOS): use Open Anyway as described under Install.
  • The file will not open: close it in other programs (MIB Studio, HDFView, Python) first. A file that is still being recorded cannot be opened.
  • Sizes look wrong: check the pixel-to-micron factor in the status bar. "(fallback)" means the file recorded none; set the right value under File ▸ Preferences….
  • Check for updates fails: the computer needs internet access to updates.yofo.bio. You can always install a newer version by hand from the GitHub Release.