FlouPlot

     3D-Visualization Tool
     for Time-Resolved
     Fluorescence Data

User's Manual
     Vers. 1.6



Table of Contents

     1. Introduction

     2. Installation and First Steps

        2.1 Up-To-Date Drivers
        2.2 Known Problems

     3. The FluoPlot Window and Main Menu

        3.1. The Files Menu
             3.1.1. File | Open
             3.1.2. File | Add
             3.1.3. File | Info on Data Loaded
             3.1.4. File | Load Spectral Correction
             3.1.5. File | Exit

        3.2. The View Menu
             3.2.1. View | View Type
                    3.2.1.1. View | View Type | 3D-View
                    3.2.1.2. View | View Type | Top-View
             3.2.2. View | Projection
                    3.2.2.1. View | Projection | Orthographic
                    3.2.2.2. View | Projection | Central
             3.2.3. View | Apply Spectral Correction
             3.2.4. View | Show Height Lines
             3.2.5. View | Z-Axis-Scale
                    3.2.5.1. View | Z-Axis-Scale | Linear
                    3.2.5.2. View | Z-Axis-Scale | Logarithmical
             3.2.6. View | Scale Raster Grids ...
             3.2.7. View | Counts Color Map ...
             3.2.8. View | Mapped Backplanes
             3.2.9. View | Background Color ...

        3.3. The Windows Menu
             3.3.1. Windows | Cascade
             3.3.2. Windows | Tile Horizontally
             3.3.3. Windows | Tile Vertically
             3.3.4. Windows | Minimize All
             3.3.5. Windows | Arrange Minimized
             3.3.6. Windows | <Window Name>

        3.4. The Help Menu
             3.4.1. Help | Content
             3.4.2. Help | Index
             3.4.3. Help | Search
             3.4.4. Help | About FluoPlot ...

     4. The Main Plot Window

        4.1. Scaling the Plot
             4.1.1. Z-Axis Auto Scale
             4.1.2. Customized Scale on All Axis

        4.2. Mouse Cursor Modes
             4.2.1. Rotate Plot
             4.2.2. Drag Planes
             4.2.3. Select Zoomed Region
             4.2.4. Move Zoomed Region

        4.3. Zoom Functions
             4.3.1. Zoom In  ( x 2 )
             4.3.2. Zoom Out (Last Zoom)
             4.3.3. Un-Zoom  ( x 1 )

        4.4. Export Functions
             4.4.1. Export BMP to File
             4.4.2. Export ASCII to Clipboard
             4.4.3. Export ASCII to Origin File

     5. The Intersection Windows "Spectral Distribution", "Fluorescence Decay"

     6. The Data Grouping Windows "TRES Plot", "Multi Decays Plot"

        6.1. Selecting the Group Colors
        6.2. Showing the Legend

     7. Table of Shortcuts

        7.1. File Functions
        7.2. View Functions
        7.3. Help Functions
        7.4. Mouse Cursor Modes and Mouse Functions


1. Introduction

FluoPlot is an interactive 3D-visualization tool for time-resolved fluorescence
data as it comes from TCSPC systems like TimeHarp, NanoHarp, PicoHarp and
HydraHarp by PicoQuant. It is designed to support your work in respect of
analysis, illustration and documentation and in providing many useful graphics
and data import and export facilities. It also interfaces with the fluorescence
decay analysis package FluoFit.

It uses modern hardware acceleration with OpenGL and GLScene to provide a
flexible and fast animated visualization of your data. Intuitive navigation and
convenient control by mouse or keyboard as well will let you feel familiar
after a short time of customization.



2. Installation and First Steps

FluoPlot comes as supporting software for your hardware and software products
dealing with time resolved fluorescence data. It provides its own installation
environment thus allowing an installation apart from the data acquisition
software e.g. on a computer, where you analyse and document your data. The
installation wizard will lead you through the installation process step by step
as you are used to from most other software systems for MS–Windows(tm).

| Note:   It is possible to install FluoPlot on your local area network and run
|         it from any computer, from which you are allowed to access the part of
|         the file system where FluoPlot resides. Even though you could simply
|         start the FluoPlot.EXE without installing, you should at least invoke
|         FluoPlot.REG by means of a simple double click once before you run it
|         first time. This provides the program with proper starting conditions.

These are e.g. pre-stored default positions, color schemes etc. This is also a
means of resetting stored options to the defaults if you should ever spoil your
settings by incident or mistake. To preserve your own visual settings for a po-
tential restore use the batchfile "SaveMyFluoPlotSettings.bat", shipped with
the FluoPlot software. Running this batch from the explorer(tm) or invoking it
from the commandline will create an ASCII-readable file. By default it will be
named "MyFluoPlot.reg", a different filename may be specified as the first
parameter in the commandline. The file now will contain your current settings.
By double clicking this file these settings will be restored to the registry.


2.1 Up-To-Date Drivers

Even though installation is as easy as could be, you have to take care of an
important detail before you can work with FluoPlot in the fastest way:

FluoPlot makes extensive use of OpenGL features which came first with OpenGL
version 1.5. If your graphics device drivers don't support OpenGL or come with
a version prior to V1.5, you might observe deficiencies in the visual presen-
tation of your data. You may find out which version of OpenGL is actually
installed on your computer invoking GLInfo2.EXE from the FluoPlot installation
directory.

 | Note:   Be sure you have installed the latest driver package for your
 |         computer's graphics card provided by the manufacturer on the
 |         internet or shipped on CD. Although most graphic cards will be sup-
 |         ported by Microsoft's generic drivers, it is almost always necessary
 |         to update, since most of the generic drivers only support subsets of
 |         the actual capabilities (version 1.1).


2.2 Known Problems

Now that you have taken care of the driver installation, everything should
be ready to go. However, there are a few graphics hardware products, which cause
problems with OpenGL.

If you have a graphics card from the ATI(tm) Radeon family installed on your
computer and you operate it with the latest generation drivers as recommended,
you may notice that either the color mapping is spoiled (the main plot is
colored monochrome and indistinguishable) or - if the hardware acceleration is
off - changing the view on your data gets beyond any reasonable waiting time
and the plots are jerking and flickering during movements.

This is a problem known by ATI but not yet solved. If this doesn't collide with
other requirements, it could possibly be a work-around to change to an older
driver generation. As far as known to us, the last driver version that came
without this bug was version 6.5 and may be downloaded from

     "http://ati.amd.com/support/drivers"

where you have to choose your system specifica as if you intend to download the
latest driver version. Then look for the link

     "Previous Drivers and Software"

and choose version 6.5. Before you can install this driver you have to remove
the newer driver from the system. Follow the instructions given in

     "737-20561: Removing Old ATI Software"

in the knowledge base from the custom care site at


     "https://support.ati.com/ics/support"

 | Note:   All information given above, notably site locations are beyond
 |         control of PicoQuant GmbH and may change without notification.



3. The FluoPlot Window and Main Menu

Upon starting FluoPlot the main window appears with its main menu. Nearly
everything that takes effect on more than one child window may be controlled
through the main menu. Some of the menu items are provided
additionally as speed buttons for convenience. These buttons may be
found below the line with the main items. The main items are:

          Files,
          View,
          Windows and
          Help.

The main menu items can be activated by pressing the
<Alt>-key plus the first letter of the intended menu item (F, V, W or H resp.).
The hidden drop down submenu opens and provides a list of submenu actions.


3.1. The Files Menu

Clicking on the main menu item "Files" the following submenu will open:

          Files
          |  Open                       Ctrl+O
          |  Add                        Ctrl+A
          |  Info on Data Loaded        Ctrl+I
          |  ---------------------------------
          |  Load Spectral Correction   Ctrl+S
          |  ---------------------------------
          |  Exit                       Alt+F4


Some of the menu items may or may not be disabled (grayed). For most of the
items this depends on the phase of work, that you're actually in at the moment.
This goes not for "Add", which is always grayed out, for this feature will not
be supported by the FluoPlot version at hand. Future versions may come with the
capability to compose the data shown from more than one file.


3.1.1. File | Open

Clicking  "File | Open"  or the appropriate speed button with the mouse or
entering  <Ctrl>+O  from the keyboard, an open dialog with extended preview
functionality appears. Users, who are familiar with FluoFit will recognize the
similar look and feel of this dialog.

On the left, there is an ordinary file selection box, which you know from
nearly any file oriented program running on Windows(tm). Clicking on a file
containing proper time correlated single photon counting (TCSPC) data, the
file is opened for a preview.

The right hand area offers the preview of the desired data. You may either
observe the stored decays curve by curve (Preview) in both, linear or
logarithmical scale or inspect the data set attributes (File Info) stored with
the curves, depending on the tab you activate.

If you finally click on the button "Open" or strike <Alt>+O the selected
dataset will be loaded and all previously loaded curves are removed from
memory. The whole data set will be displayed in the main plot window, the
intersection planes will stand on index zero and the grouping plots are
initialized with some reasonable defaults (just to get an idea of the data).



3.1.2. File | Add

(Not supported in this version!)

Clicking  "File | Add"  or the appropriate speed button with the mouse or
entering  <Ctrl>+A  from the keyboard, the upper mentioned open dialog will
show up once again, with all its capabilities. Clicking on the button "Open"
or stroking <Alt>+O, the selected dataset will be checked on compatibility and
added to all previously loaded curves, if they match. If they don't, you will
get a pop-up message and the add process will be stopped as if it was never
started.


3.1.3. File | Info on Data Loaded

Clicking  "File | Info on Data Loaded"  or the appropriate speed button with
the mouse, or entering  <Ctrl>+I  from the keyboard, an info-dialog opens. It
provides the same information as the preview / file info section in the
Open-dialog did, with the future (coming with the "Add" command) additional
capability of showing info on either loaded file respectively. You then may
choose from a list of all loaded files.


3.1.4. File | Load Spectral Correction

Since the recording hardware has a typical sensitivity as a function over
spectrum, there is an opportunity to equalize the spectra. This is to be done
by loading a file with the appropriate Spectral Correction Data (*.SCD).
Clicking  "File | Load Spectral Correction"  or the appropriate speed button
with the mouse or entering  <Ctrl>+S  from the keyboard, an open dialog
appears. Clicking on the button "Open" or stroking <Alt>+O, the selected
correction data file will be loaded.

 | Note:   This menu item is only to load the data, but doesn't apply it. To
 |         apply/un-apply the spectral correction use the designated command
 |         "Apply Spectral Correction" (refer to the "View" menu).

Most producers provide this data in different formats. FluoPlot expects the
data in simple ASCII-readable form. It may contain comments, led by the hash
mark character ('#').

There are two equivalent forms to provide the necessary information:
     a) as a list of spectral sensitivity factors or
     b) as a list of spectral correction factors.
The SCD-File has to be headed by a designator which kind of data it contains.
It reads either
                FACTORS = CORRECTION
             or
                FACTORS = SENSITIVITY
respectively. This designator will be followed by a non-ambiguous list of
numeral pairs, first value standing for the wavelength in nm, second for
the respective factor (both as integer or fixed point real) which may or may
not be sorted by wavelength.

Thus the following examples are equivalent:

               #FluoPlot Spectral Sensitivity Data
               #
               FACTORS = SENSITIVITY
               #  wavelength sensitivity_factor
               600        0.076923
               610        0.222222
               615        0.4
               620        0.666667
               627.5      1
               642        0.666667
               652        0.4
               666        0.2
               684        0.095238
               688        0.08
               694        0.095238
               706        0.041667
               # ...
or

               #FluoPlot Spectral Correction Data
               #
               FACTORS = CORRECTION
               #  wavelength correction_factor
               600       13.0
               610        4.5
               615        2.5
               620        1.5
               627.5      1
               642        1.5
               652        2.5
               666        5.0
               684       10.5
               688       12.5
               694       15.2
               706       24.0
               # ...



3.1.5. File | Exit

Clicking  "File | Exit"  with the mouse or entering  <Alt>+F4  from the
keyboard terminates the program without further questions. All files you might
have loaded will be closed.


3.2. The View Menu

Clicking on the main menu item "View" the following submenu will open:

          View
          |  View Type                            >
          |  Projection                           >
          |  --------------------------------------
          |  Apply Spectral Correction Ctrl+Alt+S
          |  Show Height Lines         Ctrl+Alt+H
          |  Z-Axis-Scale                         >
          |  Scale Raster Grids ...
          |  --------------------------------------
          |  Counts Color Map ...
          |  Mapped Backplanes         Ctrl+Alt+B
          |  Background Color ...


Some of the menu items may or may not be disabled (grayed). This depends on the
phase of work, that you're actually in at the moment. Items which are followed
by an ellipsis ("...") will open a specialized form, those which are followed
by an arrow to the right (">") will open a submenu.


3.2.1. View | View Type

This is to change the view type for the main plot window. This menu item will
open a submenu:

          View
          |  View Type                 >
          |  |  3D-View     Ctrl-Alt-3
          |  |  Top-View    Ctrl-Alt-2
          | (...)

The respective view type currently active is marked with a tick in front of the
type name. The respective speed button will be shown lowered (pressed) and
highlighted.


3.2.1.1. View | View Type | 3D-View

Clicking  "View | View Type | 3D-View"  or the appropriate speed button with
the mouse or entering  <Ctrl>+<Alt>+3  from the keyboard will change the view
type for the main plot window to 3D-view. This view offers the opportunity to
look at your data in 3D-projection from any angle you might want to. Changing
back from top to 3D-view, the last orientation of the data cube will be
restored.

This is probably the best way to visualize photon counts information which will
not only be coded with the current color map, but also in Z-axis height.


3.2.1.2. View | View Type | Top-View

Clicking  "View | View Type | Top-View"  or the appropriate speed button with
the mouse or entering  <Ctrl>+<Alt>+2  from the keyboard will change the view
type for the main plot window to top-view (2D-view). This view offers the
opportunity to look at your data right from the top. Photon counts information
will still be interpretable due to the coding with the current color map but
Z-axis information will be occluded. Changing from 3D- to top-view, the last
orientation of the data cube will be stored.

This is probably the best way to recognize dependencies between time and
wavelength behaviour since no 3D-occlusion may cover the desired information.


3.2.2. View | Projection

This is to change the projection type for the main plot window. This menu item
will open a submenu:

          View
          | (...)
          |  Projection                  >
          |  |  Orthographic  Ctrl-Alt-O
          |  |  Central       Ctrl-Alt-C
          | (...)

The respective projection type currently active is marked with a tick in front
of the projection name. The respective speed button will be shown lowered
(pressed) and highlighted.


3.2.2.1. View | Projection | Orthographic

Clicking  "View | Projection | Orthographic"  or the appropriate speed button
with the mouse or entering  <Ctrl>+<Alt>+O  from the keyboard will change the
projection type for the main plot window to orthographic. This means the data
cube is viewed along parallel lines that are perpendicular to the plane of the
viewer. This is to facilitate the reading of the labels in the depth of the
space, because all parallels are isometric.


3.2.2.2. View | Projection | Central

Clicking  "View | Projection | Central"  or the appropriate speed button with
the mouse or entering  <Ctrl>+<Alt>+C  from the keyboard will change the
projection type for the main plot window to central. This means the data cube
is viewed along a ray beam focused in one single point (the camera). This is
the more natural type of projection, which produces pictures, in the way we are
used to see. This is to facilitate the reading of the spacial relationships.


3.2.3. View | Apply Spectral Correction

Clicking  "View | Apply Spectral Correction"  or the appropriate speed button
with the mouse or entering  <Ctrl>+<Alt>+S  from the keyboard will apply or
un-apply the spectral correction data to the time-resolved fluorescence data.

This item is enabled if and only if a set of spectral correction data was
preliminarily loaded. If it is active, the item is marked with a tick in front
of the item's text and the respective speed button will be shown lowered
(pressed) and highlighted.

Applying multiplies all photon counts with the appropriate correction factor of
the respective wavelength (if necessary interpolated). Un-applying restores the
original counts.

 | Note:   Spectrally corrected data is no longer following the presumed
 |         Poisson statistics and therefore is not applicable for a proper
 |         parameter fit. This is the reason why there will be an alerting
 |         label in all plot windows. You may still export your data, but be
 |         cautious not to jump to statistical conclusions!


3.2.4. View | Show Height Lines

Clicking  "View | Show Height Lines"  or the appropriate speed button with the
mouse or entering  <Ctrl>+<Alt>+H  from the keyboard will apply or un-apply iso-
height lines to the data profile in the main plot window. If this item is
active, the item is marked with a tick in front of the item's text and the
respective speed button will be shown lowered (pressed) and highlighted.


3.2.5. View | Z-Axis-Scale

This is to change the scaling of the Z-axis for all plot windows simultaneously.
This menu item will open a submenu:

          View
          | (...)
          |  Z-Axis-Scale                 >
          |  |  Linear         Ctrl-Alt-N
          |  |  Logarithmical  Ctrl-Alt-G
          | (...)

The respective Z-axis-scale currently active is marked with a tick in front of
the scale name. The respective speed button will be shown lowered (pressed) and
highlighted.


3.2.5.1. View | Z-Axis-Scale | Linear

Clicking  "View | Z-Axis-Scale | Linear"  or the appropriate speed button with
the mouse or entering  <Ctrl>+<Alt>+N  from the keyboard will change the
Z-axis-scale to linear. This will also affect the scaling grid for the height
lines.


3.2.5.2. View | Z-Axis-Scale | Logarithmical

Clicking  "View | Z-Axis-Scale | Logarithmical"  or the appropriate speed
button with the mouse or entering  <Ctrl>+<Alt>+G  from the keyboard will
change the Z-axis-scale to logarithmical. This will also affect the scaling
grid for the height lines.


3.2.6. View | Scale Raster Grids ...

Clicking  "View | Scale Raster Grids ..."  or the appropriate speed button with
the mouse will open a form where you may choose the actual raster grids for
both the linear and the logarithmic scaling. The actual selected grids are
shown in a white horizontal bar which respectively stands for a single decade
in linear or logarithmical graduation.

 | Note:   You always define both in the same step, the logarithmical and the
 |         linear grid, since you are allowed to switch between them at any time
 |         you want.

In addition to the grid definition you can decide, if the labeling will be
reduced to whole decades in logarithmical scaling. To do so, check the check
field below the combo box  with a tick.


3.2.7. View | Counts Color Map ...

Clicking  "View | Counts Color Map ..."  or the appropriate speed button with
the mouse will open a form where you may choose from pre-installed color maps
by name, alter them or construct your own new ones.

The pre-installed color maps are shown as a name list in a combobox. Selecting
an existing map will present it in the map presentation box right below this
combobox and update the table of position/color pairs right at the bottom of
the form. You may add new maps by simply type a new name into the edit field of
the combobox. To delete an existing map select it from the list and press the
delete button on the right side of the combobox. You will be asked once if you
really want to delete this map. If you agree, it will be destroyed without any
chance to undo; so be careful in deleting color maps.

Within any map you may alter a given color by clicking on the color selection
panel below the map presentation box and select a new color with the standard
color selection dialog. Which color of a given map you are about to alter will
be visualized through the position of the trackbar pointer and the highlighted
row in the definition table below. Altering a color results in altering the map
color definition table.

With the exception of the edges you may alter the in map position of any color
as well. This is be done by simply dragging the trackbar pointer to the desired
position. The range over which this position may be altered is delimited
through the neighbours of the color. New color/position pairs may be created by
right clicking in the row which follows the desired table position of the new
pair. The new element will be added preceding the clicked line with the same
color as its successor and his position decremented by one-tenth of a percent
(i. e. pro mille [‰]).

 | Note:   If necessary, you can enlarge the resolution of the track bar
 |         pointer by simply widen the whole form. The map presentation box and
 |         the track bar as well will be resized and thus allow to define the
 |         desired position more precisely.


3.2.8. View | Mapped Backplanes

Clicking  "View | Mapped Backplanes"  or the appropriate speed button with
the mouse or entering  <Ctrl>+<Alt>+B  from the keyboard will apply or un-apply
the mapped background of all intersection plots. If the item is active, it is
marked with a tick in front of the item's text and the respective speed button
will be shown lowered (pressed) and highlighted.


3.2.9. View | Background Color ...

Clicking  "View | Background Color ..."  or the appropriate speed button with
the mouse will invoke a standard color selection dialog from which you may
select a background color for all plot windows.

 | Note:   Be careful with dark colors: Even though the curves might abound a
 |         little more, the labelling will stay black and so probably harder to
 |         read.


3.3. The Windows Menu

Clicking on the main menu item "Windows" the following submenu will open:

          Windows
          |  Cascade
          |  Tile Horizontally
          |  Tile Vertically
          |  Minimize All
          |  Arrange Minimized
          |  ------------------------
          |  <List of all windows>

This is a Windows(tm) standard menu and should be familiar from many other
programs in the Windows world. Additionally all currently available windows are
listed beneath the separator bar. The tick in front of the window name states
that the window is currently active in the FluoPlot main window. If you click a
checked window, it will be minimized, if you do so for an unchecked window, it
will be activated and shown on its last position.

3.3.1. Windows | Cascade

Clicking  "Windows | Cascade"  or the appropriate speed button with the mouse
will cascade all non minimized windows from the upper left corner to the lower
right so that the title bars all are visible.


3.3.2. Windows | Tile Horizontally

Clicking  "Windows | Tile Horizontally"  or the appropriate speed button with
the mouse causes Windows to re-arrange all non minimized windows as horizontal
stripes. If there are too many windows opened, Windows will divide the
horizontal stripes and arrange more than one window in each stripe.


3.3.3. Windows | Tile Vertically

Clicking  "Windows | Tile Vertically"  or the appropriate speed button with
the mouse causes Windows to re-arrange all non minimized windows as vertical
stripes. If there are too many windows opened, Windows will divide the vertical
stripes and arrange more than one window in each stripe.


3.3.4. Windows | Minimize All

Clicking  "Windows | Minimize All"  with the mouse minimizes all windows and
arranges arranges their minimized headers in the lower left corner of the main
window.


3.3.5. Windows | Arrange Minimized

Clicking  "Windows | Arrange Minimized"  with the mouse will re-arrange the
minimized windows in the lower left corner side by side. This will also happen
on resizing the main window.


3.3.6. Windows | <Window Name>

Beneath the separator bar all currently available windows are listed. Active
windows (non minimized) are marked with a tick in front of their name. You may
toggle the window's status by clicking on its name: Active windows become
minimized, minimized windows become active again. They will re-appear on the
same position they occupied last time they were neither minimized nor maximized.


3.4. The Help Menu

Clicking on the main menu item "Help" the following submenu will open:

          Help
          |  Content              Ctrl+F1
          |  Index                F1
          |  Search               Shift+F1
          |  ----------------------------------
          |  About FluoPlot ...   Shift+Ctrl+I


3.4.1. Help | Content

Clicking "Help | Content" with the mouse or entering  <Ctrl>+<F1>  from the
keyboard will open the online help with the content page.


3.4.2. Help | Index

Clicking "Help | Index" with the mouse or entering  <F1>  from the keyboard will
open the online help with the index.

3.4.3. Help | Search

Clicking "Help | Search" with the mouse or entering  <Shift>+<F1>  from the
keyboard will open the online help with the full text search page.


3.4.4. Help | About FluoPlot ...

Clicking "Help | About FluoPlot ..." with the mouse or entering  <Shft>+<Ctrl>+I
from the keyboard will open the About-dialog. Here you read the actual version
and build number of the program. Please refer to this number, if you ever
contact PicoQuant GmbH for problems with this software.



4. The Main Plot Window

This window is designed to give you a survey of the data and a view at it as a
whole. All data will be presented inside of a cube, (X-axis as time, Y-axis as
wavelength and Z-axis as counts,) which you can let rotate around the Z-axis to
whatever angle you want and between -90° and +90° around either two axes. You
may change back and forth between 3D and top view (2D) whenever you like to.
The last 3D orientation will be stored on change to 2D view and restored when
changing back.

The data view is enriched by two semi-transparent planes that you can move
within the cube. The red plane moves in parallel to the time axis, the green
one in parallel to the wavelength axis. These planes are useful multi purpose
tools. They can work

     a) as data cursor on time- or wavelength-axis respectively, since their
        distinct position is identified in either color beneath the plot box.

     b) as a means to determine an intersection through the data in either
        orientation. The red plane determines a moment in time, where you may
        look at the actual spectrum, the green plane determines a distinct
        wavelength, for which you may have a closer look at the decay curve.

     c) to define a fixed point at the intersection of the two planes. This
        point stays unstretched and unmoved if you zoom into the data with the
        command "Zoom In ( x 2 )".


4.1. Scaling the Plot

Below the plot box, you find a group of radio buttons which let you choose
between three different scaling modes for the Z-axis (i.e. counts) and six spin
edit fields to control the borders of the data cube, a pair for either direction.
The spin edit fields for the counts axis are disabled or enabled respectively
depending on the chosen auto scale mode for the Z-axis.


4.1.1. Z-Axis Auto Scale

The standard mode for Z-axis auto scaling is  "on total data, incl. IRF". This
is because the intersection windows will follow the scaling of the main plot
and the "Fluorescence Decay Plot" may additionally display the IRF. Your data
set therefore may or may not fill the whole cube, depending on the maximal
counts in the data curves and in the IRF, as well as on the region, if zoomed.

If you zoomed into the data set, you might want to stretch the counts scale
until the dynamics of the data in display covers the whole cube. This is done
with the radio button "on displayed region". This mode is ignoring the IRF and
therefore might let the IRF exceed or fall below the borders of the intersection
plots.

Of cause you may want to set the Z-axis borders to your own, special require-
ments (let's say e.g. to full decades). To do so, you have to switch "off" the
whole auto scaling mechanism. This - and only this - enables the pair of spin
edit fields dedicated to set the Z-borders of the data cube. You are free to
determine the range between 1 and ten times the maximum of all counts (the IRF
included).

It might happen for a zoomed region, that there is no data at all to display
within the distinct range you chose. Don't be irritated by this phenomenon but
switch back to auto scale mode "on displayed region" or "on total data" to re-
orientate.


4.1.2. Customized Scale on All Axis

As described in the previous paragraph, you may set the borders of the Z-axis
to any reasonable value you might want, if the auto scale mode is "off". In
contrast to this behaviour there is no conditional restriction for the other
axes. You are free to set the borders of the data cube in time and wavelength
whenever you want to, separately and independent, but only within the limits of
the given data set. You may not exceed the minimum resp. maximum index because
there is no data defined outside to display.

The changes to the data cube's borders are the same as zooming in the semantics
of the program and will therefore be stored in the zooming history. If you fail
to enter a proper range for either axis, you may recover form this accident by
simply invoke "Zoom Out (Last Zoom)".

 | Note:   To save dynamic memory space, multiple changes to the range of the
 |         same axis will be treated as one in zoom history! Therefore the
 |         "Zoom Out (Last Zoom)" command sometimes may show a kind of
 |         unexpected (but still reasonable) behaviour.


4.2. Mouse Cursor Modes

While working with FluoPlot you will occasionally change the working mode in the
plot boxes. You do so by use of the right mouse context menu or by striking
the appropriate shortcut. To unambiguously visualize the current working mode
after changing it or when entering the plot box with the mouse pointer, the
mouse cursor will change its shape to an adequate form.


4.2.1. Rotate Plot

In this working mode the mouse cursor shows a stylized data cube with rotation
insinuating arrows. Change to this working mode by selecting "Rotate Plot" from
the right mouse context menu or typing  <Ctrl>+R  from the keyboard. If you
hold and drag left clicking with the mouse, the cube will follow the movements
of the mouse.

Up/down will cause a pitching movement around the horizontal axis through the
middle of the cube, right/left will cause a turning movement around the
vertical axis through the middle of the cube. You don't have to point somewhere
within the cube: anywhere inside the plot box will be valid.


4.2.2. Drag Planes

In this working mode the mouse cursor shows a stylized intersection plane with
linear movement insinuating arrows and a cross hair as hot spot at the tip
of the lower arrow. Change to this working mode by selecting "Drag Planes" from
the right mouse context menu or typing <Ctrl>+D from the keyboard. If you left
click on either plane and hold the mouse button, yellow moving direction arrows
appear in the plot and the plane will be highlighted.

Dragging the mouse in the direction of the yellow arrows will take the plane
with it, other directions will result in a slower speed or no movement at all.
You have to hit the respective plane exactly to identify it, successful
identification is visualized by a highlighted plane.


4.2.3. Select Zoomed Region

This working mode is only available in top-view (2D). In 3D-view it is always
disabled. If active, the mouse cursor shows a stylized looking glass with a
cross hair as hot spot in the middle. Change to this working mode by selecting
"Select Zoomed Region" from the right mouse context menu or typing <Alt>+Z from
the keyboard. If you left click and drag on the data region, a blue dotted
rubber band will span a rectangle from the first mouse down position to the
current mouse pointer position, anticipating the later zoomed view region.

If you started this by mistake you have two choices:
  a) First you could reduce the rubber rectangle to the smallest you could reach
     (reduce area to zero). This would be recognized as erroneous and therefore
     ignored on release of the mouse button.
  b) You could simply invoke "Zoom Out (Last Zoom)" to recover from the zoomed
     in position.


4.2.4. Move Zoomed Region

This working mode is only available with previously zoomed view. If active, the
mouse cursor shows a stylized looking glass with a cross hair as hot spot in
the middle and movement insinuating arrows in the four edges. Change to this
working mode by selecting "Move Zoomed Region" from the right mouse context
menu or typing <Ctrl>+M from the keyboard.

If you hold and drag left clicking with the mouse, yellow moving direction
arrows appear in the plot and the data region will follow the movements of the
mouse panning through the data cube. You don't have to point somewhere within
the cube: anywhere inside the plot box will be valid. Since this function was
particularly intended to be used in top-view, it works the better, the steeper
you look onto the data region.


4.3. Zoom Functions

Since the Z-axis with its auto scaling mechanism follows special rules, zooming
in FluoPlot means most commonly reducing the ranges of the time and the
wavelength axes. There are different ways to do so, as you could invoke the
"Select Zoomed Region" command or directly set the scaling borders in the main
plot window. But there is an easier way to reach the goal, the usage of the
"Zoom In  ( x 2 )" command.


4.3.1. Zoom In  ( x 2 )

If you select  "Zoom In  ( x 2 )"  from the right mouse context menu or type
<Ctrl>+Z on your keyboard, this function will be invoked. It simply does what
you might expect: It halves the ranges in both directions, time and wavelength.

But it is working on a special offset since it uses the intersection point of
the red and the green plane as a fixed point. This point keeps its position, while
all other points double their distance to the fixed point - the plot is sized by
factor two. From now on, a part of your data lays outside the data cube. You
could move to this parts of the plot using the command "Move Zoomed Region".


4.3.2. Zoom Out (Last Zoom)

This is simply a "undo last step" function for all kind of zooming activities.
Every scale size changing operation will be logged dynamically in the zooming
history. If you select  "Zoom Out (Last Zoom)" from the right mouse context
menu or type <Ctrl>+<Alt>+Z on your keyboard, the current settings will be
replaced by the last ones, refreshing all plots on the older positions.


4.3.3. Un-Zoom  ( x 1 )

This command resets the scales of all axes and the zooming history, too. It may
be invoked by selecting  "Un-Zoom  ( x 1 )" from the right mouse context menu
or typing <Shift>+<Ctrl>+Z on your keyboard.


4.4. Export Functions

Even though FluoPlot is not designed to newly calculate or alter data but rather
to visualize them, it comes with some export functions. They work always on the
currently visible region. Therefore you could use FluoPlot as a means of
reviewing big data files and reducing the data overhead of noisy, irrelevant
data before and behind the interesting region to save much time for analysis.

 | Note:   FluoPlot is not designed to export binary data formats!
 |         It exports data solely in ASCII or graphics as bitmap files.

But since FluoFit is able to read the clipboard format of all windows
containing the plots of decays you can re-import the manipulated data. The only
values lost will be the absolute time and wavelength components.

The spectral plot windows on the other hand will export all relevant data,
including the absolute time and wavelength information but could not been re-
imported by FluoFit because they carry less information to just illustrate very
small slices in time.


4.4.1. Export BMP to File

Every plotting box may export its image as a bitmap file. This may be invoked
by selecting  "Export BMP to File" from the right mouse context menu and then
taking a choice from the list of resolutions. Remember that every doubling of
the resolution increases the demands in time- and disk space by four. To export
a full sized window in highest resolution will take quite a lot of time...

 | Note:   The hint on spectrally corrected data will not be rendered into
 |         the bitmap, since it is just an internal flag to your remembrance.


4.4.2. Export ASCII to Clipboard

Every plotting box may export its data to the clipboard. This might be invoked
by selecting  "Export ASCII to Clipboard" from the right mouse context menu or
typing <Ctrl>+C on your keyboard. The format is either FluoFit readable for
decay plots or the special format as aforementioned for spectral plots with a
complete set of data components.


4.4.3. Export ASCII to Origin File

Every plotting box may export its data to a ASCII-file designed to be readable
by Origin(tm) and other table oriented programs. This might be invoked by
selecting "Export ASCII to Origin File" from the right mouse context menu or
typing <Ctrl>+G on your keyboard.

The format is separated by tabs, first row containing the columns titles,
second row containing the curves parameter (time or wavelength respectively),
third line is empty. All following lines contain the photon counts.

For spectral plots, each line is commencing with the wavelength. For decays the
time information is omitted.



5. The Intersection Windows "Spectral Distribution", "Fluorescence Decay"

These windows correspond directly to the red and green planes in the main plot.
If you drag a plane, the content of the respective window will be instantly
updated. The red plane as defining a moment in time corresponds with the window
titled  "Spectral Distribution"  which always shows a spectrum at the time
identified by the position of the red plane. The green plane as defining a
wavelength corresponds with the window titled "Fluorescence Decay" which
always shows the decay curve at the wavelength identified by the green plane.

The position of the either intersection is shown below the plot box on the
right hand by a spin edit field as an index directly followed by its physical
interpretation in the corresponding color. Analog to the movement of the
intersection plane you can directly enter the data index to navigate the
intersection to a desired position. With the focus inside the edit field you
can also use the <cursor up> / <cursor down> keys on your keyboard or the
mouse holding down a spin button to scroll through the data very fast. What
you will see is a quasi animated journey through your data set. Of cause this
is a lot faster for a decays intersection than for the spectral intersection
because it is most likely that your dataset has more steps in time than in
wavelength.

The intersection windows are cross referenced, since the either plot will
always show the position of the other intersection. If you look perpendicular
at the red plane in the main plot, you will see a projection of the green plane
as a vertical line and vice versa. As in the main window, the projections of the
intersection planes may be moved with the mouse. Beneath the plot box on the
left side you may read the parameter value associated with the position of the
line. This lets the intersection lines work as a kind of data cursors.

As an additional feature you may show a second curve of the same type from the
data set as a reference for dynamical comparisons. To get an idea of the use of
this reference curve, set the reference index to the value where the counts
reach their maximum. Then check the option to show the curve. It will be plotted
additionally in red. Unchecking the option hides the reference curve again.
Repeat the mentioned journey with checked reference option and see, how the
intersection curves approach the reference curve unto total convergence, then
departing again.

For the "Fluorescence Decay" window only, there is another option to show the
IRF (if there is one identified in the data set) with its corresponding
physical value if given. Unlike the reference curve it is fixed and may not be
altered. You either may show it or not.



6. The Data Grouping Windows "TRES Plot", "Multi Decays Plot"

Just as the intersection windows do, the grouping windows show intersections,
i.e. spectra or decays respectively. As opposed to the intersection windows
they are able to show parametrized groups or sets of curves. As a surplus they
may accumulate photon counts over an interval.

The look of a desired curves set depends on an ensemble of four parameters,
described as follows. In contrast to the other windows, the changes to a single
parameter will take no instant effect to the plot. The plot will not be re-
calculated as long as you don't press the "Apply"-button.

Starting at a given point (to be defined with the spin edit field "Start"), the
photon counts are totalized over a given interval (to be defined with the spin
edit field "Width") and showed in an individual curve. For the starting point
of the next curve one may define a distance to the last drawn curve (to be
defined with the spin edit field "Gap") wherein the photon counts will be
ignored. Then the next accumulation interval starts and so forth until as many
curves are plotted as desired (to be defined with the "No. of curves" spin edit
field).

All Parameters are restricted to reasonable values so that the resulting
stopping point can not exceed the allowed index range of the data set. As a
specialty you are allowed to enter even negative values for "Gap". This enables
an overlap of the totalization regions of neighbouring curves.


6.1. Selecting the Group Colors

To distinguish between the curves, you may assign a color gradient. Press the
button "Colors" and assign a starting color for the first curve and the ending
color for the last curve. The individual color of a curve will be calculated to
equidistant steps.


6.2. Showing the Legend

Additional to the color code you may identify the curves by a legend. The
legend child window will pop up if you click on the button "Legend". It
contains information on the curves colors, the data set index of their starting
position and the associated physical value.

 | Note:   The legend is not a part of the graphic, so it will not be plotted
 |         with BMP-Export.



7. Table of Shortcuts

As you learned in the previous chapters, most of the FluoPlot functions may be
controlled with the keyboard by the experienced user. We tried to define the
keyboard shortcuts as mnemonics, with keystrokes that are somehow associated
with the (name of the) function to be invoked.


7.1. File Functions

     File | Open                                            <Ctrl>+O
     File | Add            (not supported in this version)  <Ctrl>+A
     File | Info on Data Loaded                             <Ctrl>+I
     File | Load Spectral Correction                        <Ctrl>+S
    ---------------------------------------------------------------------------
     File | Exit (Program)                                  <Alt>+<F4>


7.2. View Functions

     View | View Type | 3D-View                             <Ctrl>+<Alt>+3
     View | View Type | Top-View (2D)                       <Ctrl>+<Alt>+2
     View | Projection | Orthographic                       <Ctrl>+<Alt>+O
     View | Projection | Central                            <Ctrl>+<Alt>+C
    ---------------------------------------------------------------------------
     View | Apply Spectral Correction    (toggle function)  <Ctrl>+<Alt>+S
     View | Show Height Lines            (toggle function)  <Ctrl>+<Alt>+H
     View | Z-Axis-Scale | Linear                           <Ctrl>+<Alt>+N
     View | Z-Axis-Scale | Logarithmical                    <Ctrl>+<Alt>+G
    ---------------------------------------------------------------------------
     View | Mapped Backplanes            (toggle function)  <Ctrl>+<Alt>+B


7.3. Help Functions

     Help | Content                                         <Ctrl>+<F1>
     Help | Index                                           <Alt>+<F1>
     Help | Search                                          <Shft>+<F1>
    ---------------------------------------------------------------------------
     Help | About FluoPlot ...                              <Shft>+<Ctrl>+I


7.4. Mouse Cursor Modes and Mouse Functions

     Rotate Plot                                            <Ctrl>+R
     Drag Planes                                            <Ctrl>+D
     Select Zoomed Region                                   <Alt>+Z
     Move Zoomed Region                                     <Ctrl>+M
    ---------------------------------------------------------------------------
     Zoom In  ( x 2 )                                       <Ctrl>+Z
     Zoom Out ( Last Zoom )                                 <Ctrl>+<Alt>+Z
     Un-Zoom  ( x 1 )                                       <Shft>+<Ctrl>+Z
    ---------------------------------------------------------------------------
     Export ASCII to Clipboard                              <Ctrl>+C
     Export ASCII to Origin File                            <Ctrl>+G
