Image Analyst MKII provides complex image processing tasks in a biologist-friendly manner.

Fluorescence microscopy image analysis
automation - time series - physiology

Download Image Analyst MKII


Fully functional 30-day trial version is available for download. Licensed customers please use the same link, and use your license key to permanently unlock the product.

Updates are fully compatible with all earlier versions. Installing a new version of Image Analyst MKII will not affect previously used function and pipeline parameter settings. Existing pipelines will keep on resulting the same data after the update. To update Image Analyst MKII simply download and install the latest version above.

64-bit or 32-bit? If you have 64-bit Windows, use the 64-bit version. It offers working with larger data sets and opening images with Bio-Formats faster. If you use Image Analyst MKII with Excel, the 32-bit version of Microsoft Office is required regardless the version of Image Analyst MKII. In some systems Excel may not work with the 64-bit Image Analyst MKII, in this case try the 32-bit version. Both 32-bit and 64-bit Image Analyst MKII can be run on the same computer, with the same license.

Image Analyst MKII is for research purposes only and not for diagnostic use.


We strive for your security and privacy:

  • The installer is digitally signed by "Image Analyst Software"
  • The site is daily anti-virus scanned (see SiteLock logo below)
  • Your connection is SSL encrypted.
  • Image Analyst MKII does not collect any user data. See Privacy Policy.
New in V4.1.1:
  • New features
    • Histogram and sorted bar graphs for ROI and segmentation-based analysis
    • Highlight segments corresponding to graph or histogram bars
    • Image intensity histogram with data export
    • More information in the image property box, some editable, e.g. numerically adjustable image window zoom, size and color
    • Copy/paste pipeline and function parameters as text
    • Ordinal range definitions can take 'All'
    • Rate calculation and markers on plots can be toggled
  • Core improvements
    • Faster pipeline processing of larger images
    • Improved high DPI support
    • Improved stability of pipeline processing and Prism output
  • Changes to visuals
    • Grayscale images are shown now colored based on metadata. RGB images are shown in color. To load grayscale images and use no automatic overlaying disable this feature in the Preferences/LUT page.
  • New interactive assays (see Image Analyst MKII Primer window)
    • Basic Histometry
    • Senescence-associated beta galactosidase analysis
  • 21 New pipelines including:
    • Histometric pipelines
    • Aggregate / foci counting pipelines
    • Microplate whole-well counting with automatic well positioning and debris rejection
    • Optical density measurement (micro densitometry) and succinate dehydrogenase assay pipelines
    • Quantitation of fat droplets
    • Count HE and DAB-positive nuclei in brightfield RGB images
    • Pipeline snippets for common pipeline coding examples
  • Improved pipelines
    • Single pipeline application folders were replaced with multiple thematic  ones.
    • Show color composite image
    • Tracking and velocity measurement pipelines
    • Measure fluorescence ratio in single cells using segmentation
    • Seahorse well cell count pipelines
    • Mitochondrial membrane potential pipelines
    • SA-BGAL pipeline
  • New function
    • Crop in place
  • Functions with added parameters
    • Crop - more linkage and ROI options
    • Plotting functions - Histogram option
    • Set scaling - "As recorded or custom" color option and custom color picker
  • Improvements to Membrane Potential Calibration Wizard
    • Menu-loadable dilutions worksheets for MMP calibration (see Tools menu)
    • Improved stability and verbose error messaging
    • Shorter MDC (kernel size +1) segments can be used now
    • Showing standard errors can be toggled
    • Improved graph scaling with error bars
  • Bug fixes
    • Range markers in plots
    • Export function from menu hanging fixed
    • Template matching hanging fixed
    • Fixes to run pipeline on partial microplate
    • Fixed interactive assay buttons that did not work
    • Fixed per frame intensity scaling during exporting ovrlayed images
    • Batch processing can take now single (not Multi-Dimensional Open) images
    • Multiple fixes to the internal tif reader.
    • ND2 file timing, when longer than 24h
    • Recent pipelines list cycles around properly
    • Improved Excel output of resampled time courses with gaps
    • Fixes to selecting segments and highlighting corresponding graph
  • Changes that may affect analysis results when compared to analysis performed with earlier versions of Image Analyst MKII.
    • The calculation of shape factor was changed resulting in lower values and changed gating. The updated pipelines were adjusted for this. If keeping on using old pipelines with Set Segment Classifier and shape factor set other than 0 (disabled), then decrease this value. E.g. from 0.5 to 0.3.
    • The order of RGB channel loading was changed from BGR to RGB for Windows AVI and FFMPEG (MP4, MOV, JPG, TIF…) 
    • A small change in percentile calculation is expected to cause negligible effects
    • Changes to Excel output
    • Segments deselected using ROI masking are not outputted to the table as masked columns.
    • Some header items were renamed for consistency