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Parametering and Running Image Processing Functions and Pipelines

The most basic functions are directly available in the Tools Main menu and in the toolbar :

  • Background Subtraction background subtractionbackground subtraction
  • Plot plot
  • Linescan (kymogram) generation linescan
  • Duplicateduplicate, Crop, cropCut and Merge in the Edit Main menu
  • 2D DFT filtering dftdft

To process and analyze images Image Analyst MKII provides a variety of:

  • Image processing functions (function) 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 (Pipeline) 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 (function), 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:

Propery Bar
Name of the function or pipeline
up up up up up
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Search in
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.: load button. 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 link 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 functionImage Arithmetic Single Frame  or functionTemplate 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 functionRatio 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 functionAlign Channels or functionSpectral 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 process 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:

  • process 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.

  • Run Pipeline on the main toolbar or on the Pipeline Window toolbar will execute the pipeline on the top Image Window.

  • Pipeline Automation 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 dft 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.