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.

Image Analyst MKII from version 4.2.5 is bundled with Java and no additional Java installation is required.

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? The 32-bit version of Image Analyst MKII is deprecated. You may download earlier 32-bit versions through the Version History page.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 V4.2.7:
  • Over 20 improvements, including:
    • Fixes to internal nd2 loader to correctly load files that were also problematic with the Bio-Formats reader.
    • Improved large tif and Bio-Formats loading of large images
    • New variables (see Tools/Variables and Expression Evaluation)
    • Improved z-stabilizer (tracked plane optimization option)
    • Improved Github repository handling
  • New function:
    • Replace or modify ROI/Annotation - Use the ROI tools toolbar button for additional manual ROI operations.

New in V4.2.5:
  • Over 30 improvements, including:
  • New functions:
    • Brightfield Color Deconvolution with PCA – Work with bright filed RGB images, white balance, stain normalization, stain to concentration, concentration to stain. Stain concentration images allow using standard pipelines designed for fluorescence on bright field images such as H&E staining.
    • AI Create Training Set - crop and augment annotated images
  • New features:
    • Bundled Java, no more Oracle Java needed
    • GitHub support
    • Reading labels for Keyence microplate-based images
    • Finding ROIs based on annotations and overlaps
    • Cycle around ROIs in zoomed-in images with < > keys
    • More automations supporting annotations
    • Support of multiple annotation formats, *.geojson, *.yaml+txt
    • Plot functions Histogram parameter supports cell or object counting in a variety of ways
  • Improvements
    • Speed optimizations for geometric transformations and segmentation
    • Excel data output
    • Histogram plot

New in V4.2.2:

  • Over 184 improvements, including:
  • New functions:
    • Run EXE – command line execution with image export and import, supporting passing arguments and launching multiple instances of external programs. This function is used for Cellpose and Elastix integration.
    • Create Segments from ROIs
    • Fix Vignetting (for confocal bidirectional scanning errors)
    • Set ROI Annotation
  • New pipelines:
    • “AI” flavors for histometry and select automatic ROI-based pipelines, using Cellpose.
    • Snippets
    • Updates and improvements to several pipelines.
    • Pipelines to fix hot pixels in digital camera images
  • New features:
    • ROI Annotations – named ROIs, support of PASCAL VOC annotation format
    • Frame labels – carrying original image names when multiple images are merged
    • Variables and Expression Evaluation dialog
    • New math evaluator variables added: roicount, segmentcount, imageentropy, imagemean, imageaccutance
    • String expression evaluation in pipelines can use the %param% variable now
    • Text file with a file list can be used to open recordings
    • Removal of segments close to edges
    • Faster temporal median filter
    • Time-averaged Z-stacks
    • Additional crop functions when loading large images with Bio-Formats.
    • Manual Channel Alignment
    • ROI transformation for affine, rescale, rotate functions.
    • Copy/paste of time point values, ROI annotations and Frame Labels
    • Updated histometry pipelines with new features (see descriptions)
  • Improvements to:
    •  Multi-Dimensional Open Dialog, including fixing a critical memory leak in Bio-Formats loading, fixed loading of Keyence TIF files, improvements in Z-stabilizer, improved well label handling
    •  Membrane Potential Calibration Dialog: improved constraints during ΔψM calibration resulting fewer cells rejected. Output can be baseline potentials (a bar graph) only, or ranges can be averaged, baseline can be subtracted to calculate relative changes.
    •  Prism Export, fixed scrambling of subcolumn titles when more subcolumns are added, fixed occasional failure of time course synchronization
    • Pipeline Optimizer and in Batch Pipeline Processor
    • Improved stability of video and jpg export using FFMPEG.
  • Changed behavior:
    • Baseline normalization for plots does now df/f0 and there is a separate df/f0+1 normalization.
    • Cross-correlation image now centers the origin