ImageJ

Displaying selected views in BigDataViewer

If your dataset is in a format suitable for quick visualization by BigDataViewer (e.g. multiresolution HDF5 or virtually loading), a BigDataViewer window in which selected Views can be visualized will open along with the BigStitcher main window. For other datasets, you can open BigDataViewer manually via the right-click menu by clicking Displaying › Display in BigDataViewer(on/off). If a BigDataViewer window is currently open, clicking this will close it.

For help on using BigDataViewer, you can either click Help › Show Help in the BigDataViewer window or consult the BigDataViewer documentation on this Wiki.

Toggle per-view and per-channel coloring by pressing c in the main window.

In the BigDataViewer window accompanying the BigStitcher, you can switch between color schemes by pressing c in the BigSitcher main window. A single press will switch between per-view and per-channel coloring. Pressing c repeatedly will cycle through different colors.

Displaying selected views as ImageJ images

In addition to toggling the BigDataViewer, you can also display selected views one-by-one as standard ImageJ images using the Displaying functions in the right-click menu.

• Using Displaying › Display Raw Image(s), you can open the selected views as 16-bit or 32-bit images in ImageJ.

• Using Displaying › Max-Projection, you can generate maximum-intensity projections of the selected view stacks and display them as ImageJ images.

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