Viewing and troubleshooting¶

napari¶

uv run display "/path/to/processed" --to-display fused-full --no-roi

Choose full, max-z, fused-full, or fused-max-z. Full and per-tile maximum-Z modes display processed position collections. Fused modes display the registered output. --time-range and --pos-range select visible ranges. ROI drawing is enabled by default and requires the registered fused maximum-Z image; see ROI selection.

Fiji¶

Open exported OME-BigTIFF through Plugins > Bio-Formats > Bio-Formats Importer. Use a virtual stack for datasets that cannot fit in memory. Confirm channel names, channel count, and physical spacing in the imported image.

The exporter stores UTF-8 OME-XML. Earlier files written with numeric unit references can have their metadata repaired using export-ome-tiff --metadata-only; this updates both existing fused exports without changing pixels.

Large-image browsing¶

Current exports are tiled at 512 x 512 and contain one resolution. Tiling enables region reads, but the standard Bio-Formats virtual stack requests whole planes on a cache miss. Scrolling therefore still requires substantial decoding for large planes. Bio-Formats implementation

The tifffile examples demonstrate smaller tiles and pyramidal output. Those examples do not establish an optimal tile size for Fiji. Any layout change needs measurements with the actual viewer, compression, and dataset. The exporter currently has no pyramid option.

For multiresolution OME-TIFF, Fiji's BigDataViewer Playground Bio-Formats importer provides on-demand viewing and an optional automatic pyramid. This is a separate viewer workflow from a standard ImageJ hyperstack.

Common problems¶

Symptom	Check
Unexpected fusion source	Read the selected path printed by `fuse`; pass the store explicitly.
Disconnected registration groups	Check overlap signal, channel selection, and correction limits.
Visible depth seams	Review registered placement, depth gains, and geometric support.
Resume rejects the run	Use the original settings and matching journal, or explicitly restart.
ROI cannot open	Run `fuse` to create the registered maximum-Z image first.
CUDA registration unavailable	Check GPU installation; `--require-gpu` reports failure instead of falling back.
Movie encoding fails	Check NVENC support and the installed NVIDIA driver.