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. 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. Pipeline Optimizer
      7. Interactive Ion Calibration
      8. Membrane Potential Calibration Wizard
      9. Crossbleed correction factor calculation
      10. 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 09/01/2021