Review & Post-process¶

Review tab¶

Review tab with thumbnails, the metrics table, and export actions

Open a recorded .h5 / .hdf5 file to inspect it without leaving the app. Files larger than 2 GB are fine — frames load lazily as you browse.

Browse — thumbnails load incrementally as you scroll; double-click a thumbnail (or a metrics-table row) to open the frame viewer, then use ←/→ to step frames.
Metrics table — every saved per-frame metric, with optional scatter and histogram charts over the whole dataset.
Overlays — mask/contour overlays and the ROI rectangle can be toggled on the loaded frames.
Close File releases the file handle (do this before moving or deleting the file).

Recordings made in raw recording mode (as opposed to experiments) have no masks or metrics: the tab shows a single Frames list and disables the overlay and metrics exports, but raw TIFF export still works.

Exporting¶

Export Metrics — writes <file>_metrics.csv next to your chosen location (auto-suffixed _2, _3, … rather than overwriting).
Export All — writes a folder named after the file containing metrics.csv, frame TIFFs, and chart images. For multi-image series you are asked whether to export all series frames, a range (e.g. 9-15), or skip them.
Batch Metrics / Batch Export All — select several files at once; the batch continues past individual failures and reports a summary.

The last successful output directory is remembered between sessions.

Regenerate masks (reanalyse in-app)¶

Regenerate masks… re-runs the current processing configuration over the loaded file (a frame range or all of it), an AVI, or a folder of images. The result is written to a new HDF5 file — the original is never modified — and opened in the Review tab. If no background is available, one can be synthesized from the least-changing image tiles.

Use this to rescue an experiment recorded with a bad threshold, or to compare configurations on identical input.

Standalone tools¶

For working with recordings on machines without the full app (and without Python), two tools ship separately, versioned to match the app — download the zip whose version matches Help ▸ About:

MIB_Studio_Tools_v<version>_windows.zip from https://updates.yofo.bio/stable/tools/ (manifest: tools-latest.json).

HDF5 Export (hdf5_export_app.exe, GUI) — export metrics CSV and/or frame TIFFs from a recording: pick input file, output directory, format (CSV / images / all), frame type (valid / invalid / both), and the pixel-to-micron factor.

Reanalyse HDF5 (mib_reanalyse_hdf5.exe, command line) — re-run the processing pipeline outside the app, saving per-frame intermediate images (original, blurred, diff, threshold, mask, optional overlay), an optional metrics.csv, and an optional reanalysis HDF5. Run it with --help for the full flag list; defaults match the app's processing defaults.

See docs/howto/tools.md for the full tool reference (developer docs, hosted in the repository).