Command Reference

The command reference is structured into different subjects, wich roughly correspond to the menu in the 5DViewer (accessible in ImageJ at the top or the viewer, or by right mouse click in the applet versions).

Import / Export of data

Usually the data is automatically imported at the start of View5D. It supports a number of data types: byte, 12-bit, 16-bit and floating-point (32 bit).

The 3 display windows

The main display windows (top left, top right and bottom left) show mutually orthogonal slices of a 3-dimensional dataset. These windows are linked together.

Note that context menus are available by right-clicking into one of the 3 display windows or the spectral (element) display window respectively.


A number of parameters are displayed in the text window (lower right panel). These include


Markers are an important tool for measuring positions, distances and slopes or velocity inside the multidimensional dataset. They are organized by multiple lists of ordered (connected) markers. The distance of a marker to the position of the previous marker is displayed in the text window. The slope of the line connecting successive markers is also given. This is useful for estimating the speed of movement in 2D+time datasets, where the time-direction was stacked along Z. The speed of movement in 3D datasets can be measured by setting the markers in 3D at different timepoints. The "TimeSlope" in the text-display yields the 3D speed. All markers can be dragged with the mouse after they have been set, to allow for minor corrections of their positions. A summary of all marker positions can be printed (see below: "m" in the spectral display window).
In the line-plot spectral window the spectrum on each marker is displayed in addition to the spectrum at the cross-hair position. For simultaneous display of multiple spectra, it is best to open a new list with every marker ("k") since then the markers and thus the spectra will have different colors.

Note that the intensity-related information in each marker list can be plotted in the element window (see "q" in element window).


If multiple color datasets are present or data of the same size but in different modes was acquired, the program will sort these into different “elements”. When importing the data as a 24-bit RGB image from ImageJ (either by starting the plugin) or by pressing “l” if the plugin is already running, multiple elements will result in View5D. Multiple elements can also be used working with different modes of data acquisition (MRI, PET, CT) or as results from various data processing steps (e.g. anisotropy imaging, of tau-phase and tau-mod in frequency domain fluorescence lifetime microscopy).

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For hints and suggestions, contact the author under heintzmann at gmail dot com