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.