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).
/ Export of data
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
pressing "l" (lower case "L") the data
is reloaded (if run as an
applet) or the currently active window in ImageJ is imported as a new
element. For the import to work the datasizes have to be identical to
existing datasizes (X-, Y-, Z-) in the viewer. The data-type, however,
can differ between elements.
Within ImageJ, it is important to assure that the datasizes of 4 or 5D volumes are set correctly within ImageJ: "Slices (z)" and "Frames (t)". If they are not correct, you can
do this by changing the entries in the "Image->Properies" menu of ImageJ.
an image in ImageJ possesses a non-grayscale colormap, this colormap
will be imported into the viewer and added to the menu as "user
- "s" spawns a new data-view
This is useful, if multiple slices
to be investigated simultaneously. The viewers can be resized! Press
to let the data adapt to the new size of the viewer.
lists can be exported and
imported (see Matlab support above and for
applets below: "m" in the element display and "L" in one of the views).
many systems the java runtime environment is by default not allowed to
save any data. In Linux, this security restrictions can be relaxed by
placing a file (click here)
into the user's
home directory. This file should be renamed to ".java.policy" with the
initial dot at the beginning of the file name.
- In ImageJ "X" will export data and generates an image
in ImageJ, which can
then be saved to the harddisc.
Note that exporting via "X" has different
behaviours depending on the mode, the Viewer is in and on where it is
- "X" in a viewer window and in single-channel display (see
toggle "C") will export the 16 bit internal single-color data.
The colormap is not considered here.
- "X" pressed in a viewer window when this window is in the
display will export a plot to ImageJ. This plot is immediately
displayed and can further be saved and processed. From ImageJ is is
then also possible to cut-and-paste the individual data values to other
applications such as Microsoft Excel for further processing.
- "X" pressed in a viewer window when viewing data of complex
data type will export a real-valued image of the current display mode
(abs, phase angle, real, imaginary) which can be changed by "^"
- "X" in multi-color-mode will
export a 24-bit (8 bit per RGB channel) color image considering only
the colors currently active (see "v").
- "X" pressed in the element
display (lower right corner) will export the raw-data to ImageJ. The
viewer has to be in the single color mode(via "C"). This
is especially useful for computed data such as multidimensional
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.
resets the scaling and thresholds of the currently active view
by the mouse position and outlined with a red line boarder).
does the same for all data elements (if multiple color elements are
- A mouse click sets
cross-hair to the clicked positions. The original data value underlying
the clicked pixel is indicated in the text panel (central right side).
of the crosshair are given in pixel coordinates and in a more
real-world unit (if supplied in the data). Note that by default the
position starts in the top left corner, similar to ImageJ!
- The arrow keys adjust
position of the cross-hair by exactly one voxel in the appropriate
When the cross-hair changes its position, the orthogonal slicing
positions are updated accordingly. If a click somewhere on the axial
slice is performed (top left) the sagittal view (top right) will update
to refer to the slice indicated with the green line along Y in the
axial (XY) view. Similarly
the frontal view always corresponds to the green line along X in the
view. A corresponding behavior hold for the cross-hairs indicated in
")" or "next page" "prev. page" keys allow for changes in the
and "." adjust the time when multiple time-frames are present, as does
the slider seen at the right side in this case.
and "A" enable the user to zoom in and out of the current view.
and ">" change the display scaling of the orthogonal axis.
This is very useful to alter the aspect ratio of the display,
especially since the program optimizes the available space for display
sometimes resulting in very odd aspect ratios.
zooms this view to fit the rectangular ROI defined in this view
mouse drag, adjusts the displayed sub-position in the image. This is
useful if displaying a zoomed part of the data.
toggles between displaying slices and line-plots along the
line indicated by a line of the cross-hair in another view. If
pressed in the axial (XY) view the line-scan will be along Z at the
crosshair position in this XY window. Linescans update according to
in the cross-hair position caused by pressing the arrow keys or by
- "^" runs through the different display modes (absolute
magnitude, phase angle in degree, real part, imaginary part) of data of
complex data type. Applicable for COMPLEX data type only! The currently
displayed mode will also be used for projections, all quantifications
and export functions to ImageJ.
number of parameters are displayed in the text window (lower right
panel). These include
allows the user to interactively change the scalings and units of
the coordinate and value axes.
of the cross-hair in pixel units
of the cross-hair in real-words units
of the active element at the cross-hair position in real world
of the rectangular 3D ROI in pixels and real-world units
and upper threshold of the active element
Maximum and Minimum value of this element in the currently selected ROI.
Markers are an important tool for measuring positions, distances and
slopes or velocity inside the multidimensional dataset. They are
by multiple lists of ordered (connected) markers. The distance of a
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,
the time-direction was stacked along Z. The speed of movement in 3D
can be measured by setting the markers in 3D at different timepoints.
"TimeSlope" in the text-display yields the 3D speed. All markers can be
with the mouse after they have been set, to allow for minor corrections
their positions. A summary of all marker positions can be printed (see
"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.
sets a markers in 3D at the current cross-hair position. The distance
to the preceding marker (if any) is displayed in the text window (lower
Note that the intensity-related information in each marker list can be
plotted in the element window (see "q" in element window).
deletes the currently active (as shown in white) marker.
tries to track the allready set marker throughout the stack or time
deletes all marker from the active marker position on to the end of
this marker list. This is very convenient, if the trace of a particle
is lost due to bleaching or leaving the image frame.
subtracts a Gaussian of known size and intensity determined from the
surrounding at this marker position from the data. If multiple markers
are present this is repeated for this current list.
and "0" advances/devances to the next/previous marker
aligns the display to the active track (over time or element direction only)
- "shift - cursor keys"
adjust the display positions with respect to other time or element positions
pressed at the end of a track will generate two daugther tracks with appropriate names, which can then be continued.
resets the alignment to zero
opens a menu for the current track, which allows to set names, color and the connectivity with ther tracks (parent, child1 and child2)
if pressed in a view panel or "M" in the spectral display window
a panel that lets you select several properties of the display and
behavior of markers. These include what subset to show (only active
list or all lists), and how to set the markers. The markers can either
be set directly or they automatically drag to the closest maximum pixel
in the active element. The region to search can be defined in 3D. Once
the maximum is found, another maximum search in the neighborhood is
started, such that markers can iteratively "slide" uphill over longer
distances. When this maximum is found, a further automatic refinement
(if selected in the panel) is performed on the basis of the computation
of the center of mass (or better center of intensity
COI). For this computation the "COI region" defines the voxels to
consider and the minimum pixel within this region is subtracted prior
COI evaluation. If the automatic positioning is active it will also be
after each mouse-drag of a marker.
- "&" tags/untags a marker. (This is useful for counting
purposes, e.g. to first identify nuclei in the DAPI channel, and then
tag, which ones have an associated other feature in the cell.)
opens a new list of markers, whilst setting a new marker. This will
have a new color.
changes the color of the active marker list.
deletes the whole currently active list of markers.
pressed in the spectral display window (lower right corner) prints
a list to the text window with all marker positions given in pixel and
real-words coordinates. Also included are the maximum and integrated
intensity, if the markers were generated using the "Subpixel positions
by Center of Mass" option. You should be able to cut-and-paste the
textual list from there into any editor of your system. If a marker
file name was given (Tag: markerOutFile) during startup, "m" will
OVERWRITE or create the marker file.
pressed in one of the views loads the markers from the ASCII marker
file (markerInFile as given during startup). According to the list and
marker numbers, the current marker positions will be updated. If the
list or marker is not present, it is created.
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).
and "E" step forward and backwards through the elements to define
the currently active element. In single color mode the currently
displayed element is
the active element. In general the active element defines the value
in the text display. Many operations such as automated thresholding
are carried out on the active element.
toggles between multicolor display and display of only the active
element. In multicolor mode only the elements marked for combined
display are displayed. This can be done either by defining an element
as red "r", green "g" or
blue "b" (the big letters "R,G,B" clears them from combined display) or
by marking an element for combined display with the "v" toggle.
toggles an element in and out of the multicolor overlay display.
toggles an element in and out of being displayed in a multiplicative
mode in the multicolor overlay. A channel displayed in the
multiplicative mode will have its color values being multiplied by the
so-far computed display (all elements with lower numbers). E.i. for
displaying fluorescence lifetime images, select the intensity image in
grayscale and choose the multiplicative mode and the RGB-rainbow
colormap for the lifetime information. Then the intensity image will be
displayed with a color as given by the lifetime image.
steps through the available color-maps for the active element. Some
linear, some are non-linear to enhance dim details.
toggles in and out of logarithmic display mode. Usually it is
to define the lower threshold well ("5"-"8"), since this has a major
influence on the display quality. The logarithmic mode also affects the
toggles the range indicators for the active element. If the range
indicators are active, values >= the upper threshold are indicated
in dark blue
and values <= the lower threshold in dark green. If multiple
are present, the range indicator toggle has to be changed for every
If "o" is pressed with the multi-color mode active, the range indicator
will toggle on/off for all elements. The state of the current element
dictates the state of the others.
"2" and "3","4" adjust the lower and upper color thresholds. This is
useful for enhancing the brightness and contrast of the display. Also
the line scans are affected accordingly. The color threshold just
affects the colormap. Changing it is relatively fast. If the data is to
be affected, the treshold has to be trasferred to a datathreshold (see
"!" below). Note that with the gate active, changing thresholds
automatically affect the data thresholds.
and "7","8" do the same in a finer stepping.
transfers the color thresholds to the data threshold.
adjusts the thresholds to minimum and maximum of the ROI for the
currently active element. "T" does the same for all elements. As
"i" resets the values to the initial values.
registers this element to act as a gating-mask for all other
Everything below lower and above upper data threshold (as displayed
blue when range indicators are on, see "o") is considered invalid and
from the analysis if the mask is activated (see "U" below). This
the display as well as projections and histograms for at voxels at
positions in all elements. At
the same time an element marked as gate will be used together with the
element for mathematical operations such as "+", "-" and "*". When
using gates, the color threshold is automatically transferred to the
toggles the mask activity of the mask element on and off. The mask
element (as set by "u") may differs from the active element, which
allows for a
convenient on/off toggle e.g. of an intensity mask on lifetime data
1 = intensity, channel 2 = fluorescence lifetime tau-phase).
deletes the currently active element
in the element window (lower right corner) toggles between spectral
plot display, display of multiple marker traces (the X-axis is
determined by the Track direction) and colorbars with the multiple
in the element window (lower right corner) toggles between a
and non-normalized display of multiple spectra
pressed in the spectral display spawns a bigger separate window with
the spectral display. This also frees some space for the display of
textual information. By closing the seperate window, it will be
inserted back into place.
pressed in the spectral display window will toggle the logarithmic
display in this window.
and "5"-"8" will contrast enhance the spectral plot, if pressed
spectral display window.
is a useful tool to adjust the backround level of an image to
The offset will be adjusted such, that the mean of the actual ROI in
the current element will be zero.