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The most basic functions are directly available in the Tools Main menu and in the toolbar :
, Crop, 
Cut
and Merge in the Edit Main menu 
To process and analyze images Image Analyst MKII provides a variety of:
Image processing
functions (
)
for step-by-step image processing and analysis, and for building
blocks of pipelines. These are accessible in the Main Menu between the
I/O and
Special menu items. See the list of available functions in the
Functions Glossary.
Pipelines (
)
support more complex analysis and specific biological
applications. The behavior of built-in pipelines can be
controlled through the parameter bar in a similar way to any
other image processing functions (),
and the flowchart structure of the pipeline remains hidden for
basic use. Built-in pipelines are available in the Pipelines
Main Menu. See the list of available pipelines in the Pipelines Glossary.
For expert use and editing pipelines see the
Pipeline Window page.
See a definitions of some basic image processing functions at the Image Processing Principles.
When a function or pipeline is selected in the menu, the parameters of the selected function appear in the parameter bar, below the toolbar:
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| Name of the parameters of the function or pipeline | Values of parameters | Image A | Image B | and | |||
| Images linked to the active image window are listed here | Short description of the function | Pipelines parameters and descriptions | |||||
The settings or parameters for each function or pipeline are
uniformly shown as a list in the left of the parameter bar. In the
left column the name of the parameter, in the right column the
assigned value is shown. The values can be integer, real, string
(text) and boolean (Yes or No). Strings are sometimes
selected from lists, or file names can be entered by invoking an
open/save dialog by pressing the button in the end of the input
line, when available e.g.:
.
Starting a string with = enables
parsing. Hover
the pointer over the value filed to get additional hint.
The target image (or operand) to process is
selected in the 'Image A' and 'Image B' fields.
Image windows must have the same x,y,t dimensions and must be
linked 
together to be listed for image processing in the same
context. Only image windows linked to the active image window are
listed, with few exceptions where non-linked Image B can be used,
such as
Image
Arithmetic Single Frame or
Template
Matching.
If a function has only one operand (one input image) only Image A is available for selection and multiple selection results processing each selected image one after each other.
If a function has two input images (like
Ratio calculation) set
Image A and B. If multiple images are selected, each selected
'Image A' will be processed with each selected 'Image B'.
If a function has multiple inputs, like Align Channels or
Spectral Unmixing,
images will be fed into the function in alphabetic order.
Pipelines will be executed for each Image Window checkmarked as Image A. Pipelines handle lookup of different channels internally, therefore are not controlled by the checkmarks in Image A and B.
To perform function or pipeline processing press
in the toolbar or in the Tools Main menu, or in the
context menu (right click) of the
Image Window.
Alternative ways of running pipelines:
on the main toolbar runs the pipeline selected on the parameter
bar independently on each of the Image Windows checkmarked as
Image A.
Use the 'Process this...' menu item in the context menu (right click) of the Image Window.
on the main toolbar or on the
Pipeline Window
toolbar will execute the pipeline on the top
Image Window.
on the main toolbar, on the
Pipeline Window
toolbar, or in the Multi-Dimensional Open
dialog allows automated loading of the image data followed by
pipeline execution. The pull down menu of this button allows
processing single, multiple or all stage positions in a
recording.
Default values are loaded when Image Analyst
MKII started for the first time. Default values for a function can
be revoked by the
toolbar button 'Reload Factory Defaults'.
Values of parameters are stored in the Windows System Registry when exiting Image Analyst MKII, separately for each user of the computer. Use Edit/Save Preferences to save parameters without exiting.
