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Viewer & Navigation

Scan Browser

The Scan Browser dock lists available scans in the selected folder.

  1. Open Study: Select the study folder that contains the scans. OPTARI discovers both iThera-native (Scan_ folders containing .msot files) and compatible HDF5 files (.hdf5) in it.
  2. Click a scan in the list to load it. If both an iThera and an HDF5 version of the same scan exist, OPTARI prefers the HDF5 one.
  3. Switch scans: The viewer, ROIs, and analysis docks update to the newly selected scan.

Scan Browser

The Image Viewer

  • Layer List shows every dataset in the scan as a separate layer: the US image, one or more OA reconstructions, unmixed images, etc. as well as the ROI shapes layer that contains loaded and user drawn ROIs. By default the US layer and one OA layer (recon or unmixed) are set to visible. Clicking on another OA layer will automatically select it and set the other OA layers invisible. Visibility can be controlled with the eye icon. The order of the layers can be changed by dragging them with the cursor. The currently selected layer is marked by its blue background.
  • Layer Controls adjust opacity, contrast limits, and colormap for the currently selected layer in the layer list. Layers blend multiplicatively by default for clean overlays. By default, contrast limits are adapted automatically for each slice. To finetune the contrast limits, right click on the contrast limits slider. Click the histogram button next to the contrast limit slider, to see the histogram of the selected image. If the ROI layer is selected, annotation-specific layer controls are available (see ROI Annotation).
  • Sliders at the bottom of the viewer, you can scroll through frames and channels (wavelengths or chromophores). Use the Left/Right arrow keys as a faster alternative (see Keyboard Shortcuts). The available frames and channels depend on the active layer (the OA layer selected in the layer list). This means if the selected layer has only one frame (for example because only one was reconstructed), the frame slider won't allow scrolling, even if other layers in the layer list provide more frames. The playback button next to the frame slider plays through the frame sequence automatically. Right-click it to change the playback frame rate (speed).

Tip

To set a specific, fixed contrast limit for all frames and channels instead of auto-scaling, select the respective layer from the Layer List and click the auto-contrast once button in the layer controls panel. This switches off continuous, which OA layers have on by default, and the contrast limits stay constant.

Automatic frame selection

By default, OPTARI scores every US frame for motion, using an algorithm that combines structural similarity and zero-mean normalized cross-correlation. When a new scan is loaded, it automatically selects the frame with lowest motion. This is an attempt to reduce operator variability in frame selection. The default frame is set in Settings ▸ Viewer or config.json (general.DEFAULT_FRAME_INDEX), with two kinds of motion to choose from:

  • Motion (Spectral) (default) compares the US images of the wavelengths within each frame. Tissue moving during the wavelength set misaligns the spectra and corrupts unmixing, so this picks the frame best suited for spectral analysis.

  • Motion (frame-to-frame) compares each frame with the previous and the next one, e.g. to pick a frame between breaths.

Both scores ignore the top 60 pixel rows of the US image, so the transducer and coupling area don't count as motion. This can be differ, depending on the transducer size.

The Motion widget plots both scores for every frame, with the frame with the least motion marked in green. Each score is scaled to 0–1 within the scan, so it shows where motion happens, but not how much, so the two lines should not be compared with each other or between scans.

Grid mode

Press Ctrl+G (Cmd+G on macOS) or click the grid mode icon below the layer list to view multiple layers side by side instead of overlaid. Every visible layer gets its own cell, in the same order as the layer list (top left is the top of the list). The ROIs layer is shown in its own cell too, so ROIs are not drawn on top of the images in grid mode. See Why can't I see ROIs overlaid on images in grid mode? for the reason.

Note

OPTARI does not yet support a true multi-viewer layout with synchronized annotations across separately scrolling panes. The grid mode shows layers side by side, but they share one set of dimension sliders, so it is not a real substitute. This is currently a napari limitation and will hopefully be added soon.

Alternative: It is also possible to launch OPTARI twice to have completely disentangled windows, for example to compare different scans. But keep in mind that this means ROIs and other data are not synced between the instances.

Grid Mode

For the current scan/layer's metadata, see Metadata.