Image Analyst MKIIOnline Manual
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Table of contents
  1. Getting started and more - the workflow in Image Analyst MKII
    1. Open Image sequences of one or more gray value channels
    2. The Image Window
    3. Multi-Dimensional data sets
    4. Importing images with Bio-Formats
    5. Set Image Linkage
    6. Basic and advanced image processing functions
    7. Interactive Dialogs
      1. Multi-Dimensional Open
        1. Opening multiple TIF files in folders
        2. Determine or Assign Microplate Well Names to Positions
      2. Setup DFT Filter and Optimizations
      3. Attach Intensity Gating (IMD Intensity)
      4. Attach Overlay Image
      5. Attach Overlay Text
      6. Interactive Ion Calibration
      7. Membrane Potential Calibration Wizard
      8. Crossbleed correction factor calculation
      9. Preferences
    8. Fixing imaging artifacts (Image Stabilizer, Channel Alignment, Spectral Unmixing and Lens Distortion)  
    9. Smoothing and optimizing the look of images
    10. Automation of image processing using pipelines
      1. Pipeline examples and tutorials 
    11. Using Mathematica as scripting language
    12. Annotate, overlay
    13. Define ROIs
    14. Methods of background subtraction
    15. Plot intensities, ratios of intensities
    16. Using Excel Data Window
    17. Using masking to constrain areas to plot or process
    18. Segmentation of images
    19. Plot morphological parameters
    20. Save or copy plot data in tabular format
    21. Export RGB images or movies
    22. Evaluation of expressions in function parameters
  2. Principles of processing biological data in fluorescence microscopy
    1. Fluorescence Microscopy Terms
    2. Basic Image Processing Tools
    3. Spatial filtering in Fourier domain
      1. What is Fourier domain
    4. Ratiometric Optimized Spatial Filtering
    5. Binarization, Thresholding, Segmentation
    6. Differentiation in Time and Space: Savitzky-Golay Filters 
    7. Optical Flow
  3. Functions Glossary
  4. Pipelines Glossary
  5. Protocols
    1. Background removal with high pass filtering
    2. Organelle motion assay with "Optical Flow"
      1. Protocol for image acquisition for mitochondrial motion in Elements and analysis in Image Analyst MKII
      2. Protocol for image acquisition for mitochondrial motion in Metamorph and analysis in Image Analyst MKII
      3. Protocol for image acquisition for mitochondrial motion in Zeiss LSM and analysis in Image Analyst MKII
      4. Working with Optical Flow images
      5. Fine Tuning Optical Flow
      6. Measurement of velocities and fluorescence intensities over single mitochondria
    3. Measurement of velocities and fluorescence intensities over single mitochondria
    4. Measurements of morphological properties of mitochondria e.g. length or numbers using built-in pipelines  
    5. Measurements of mitochondrial morphological properties, velocities and intensities in populations or individual mitochondria
    6. Measurement of mitochondria:cell volume ratio (Mitochondrial volume fractionator)
    7. Measurement of matrix to cytosol activity coefficient ratio for TMRM
    8. Mitochondrial swelling measurement with "ratiometric optimized spatial filtering technique" AKA "thinness ratio"
    9. Reactive oxygen species assay with normalized rate of DCFDA oxidation 
    10. Assay of levels of reactive oxygen species using DHE ratioing
    11. Assay of mitochondrial levels of reactive oxygen species using OH-ethidium rate measurement and MitoSOX:TMRM:MitoTracker Deep Red double normalization
    12. Assay of mitochondrial levels of reactive oxygen species using MitoSOX:MitoTracker Deep red end point measurement
    13. Selective measurement of mitochondrial NADH/NAD+ redox state using high pass filtering

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The online help was last updated on 4/11/2017

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