Fluorescence microscopy image analysis
automation - time series - physiology

Comparison of features to freely available open source software

  Image Analyst MKII* ImageJ or Fiji
with plugins**
Cellprofiler
Generic features
Explore multi-dimensional data sets + + -
Automate analysis flow-chart based
parallel pipeline
script linear pipeline
Time lapse analysis + marginal (see below) -
Floating point image processing all functions not all plugins supports -
Support all functions varies by plugin
Consistent user interface + - (varies by plugin) +
Time based (time lapse) analysis
Graphing intensities from multiple ROIs in time + Time Series Analyzer plugin -
Graphing fluorescence ratios in time + Old Ratio Plus plugin (2003) -
Graphing time courses with actual time (seconds) + - (frames only) -
Time metadata is always associated to frames + - -
Real time browsing ROIs and corresponding traces + - -
Filtering in time min, max, median, average, Savitzky-Golay; running and block filters mean and max using running z-projection -
Temporal differentiation + - -


Benchmarks (as seconds to complete the task)
  Image Analyst MKII* ImageJ / Fiji**  
2D median, window width = 15
2 channels, 50 frames 1024x1024 pixels***
20" 80" / 82"  
FFT (DFT) band pass filtering
2 channels, 50 frames 1024x1024 pixels***
1" (plain)
4” (with preserve edges)
14" / 22"  
more benchmarks are on the way...

*Based on Image Analyst MKII v3.1.0.Download from here.
**Based on ImageJ 1.50c, Fiji ImageJ 2.0.0-rc-39/1.50b (64-bit JRE) and plugins listed here.
***Test data set: MitoVolumeFraction1.zip from the Tutorials page. Benchmarks were done on a quad-core PC with i7-5700HQ CPU running at 3.46GHz.