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Comparison of Software

Because of the prevalence of point-and-shoot digital cameras, there is a lot of professional/consumer ('pro-sumer') software to adjust photographs, such as Photoshop. They're great for composing images for figures, but they are extremely dangerous for novices to process scientific images. Red-eye correction of your infant nephew is fine, but red-color correction on fluorescent co-localization is not. Never use their automatic features unless you know that they do identical adjustments (quantitatively) to all images of a set (e.g. z-stack), including images of control specimens. Scientific image processing software is smarter and will process a whole z-stack correctly, but not necessarily associated images of control specimens. If you're uncertain of what you're doing, don't hesitate to .

We have a lot of software, both professional/consumer and scientific, that are free for users paying the instrumentation usage fee. This is a quick comparison of the various software choices with the following categories:

  • Basic Adjustments: Adjust brightness/contrast; resize images; crop images; overlay annotations (identifying text, scale bar, etc.)
  • Basic Analysis: Calculate average brightness of whole image or of portions (rectangular/elliptical regions-of-interest, hand-traced oddly shaped regions-of-interest), scattergram plots for colocalization analysis, particle-counting (segmentation by simple thresholds)
  • Advanced Analysis: Various advanced functions such as tracking particle motions over time, trace neurons in 3D, select/process volumes in 3D
  • Programmable: Ability to automate functions, even add new capabilities, to package. Some packages, such as Volocity, offer graphical programming, allowing non-programmers the ability to automate functionality.
    Package (Mfr)ClassPurposeEase-of-use Basic Adjust-mentsBasic AnalysisAdvanced AnalysisProgrammability
    Photo software (not scientific; professional/consumer grade)
    Illustrator (Adobe)Pro-sumer Vector-based drawing; Image layout; Submission of composite images for publicationModerateYesNoNo Yes, but not scientific
    PhotoShop (Adobe) Pro-sumer Pixel-based drawing; Submission of individual images for publication Yes (basic functions) Yes No No Yes, but not scientific
    IrfanView Consumer Shareware clone of Photoshop Yes (basic functions) Yes No No No
    Scientific software, both image acquisition and image analysis
    Zen (Zeiss) Scientific Image acquisition & analysis Yes Yes Yes Yes
    (MicFac: deconvolution, FCS)
    Slidebook (3i) Scientific Image acquisition & analysis Yes YesYes Some
    (MicFac: deconvolution)
    (indirect with MatLab)
    Metamorph (Molecular Devices) ScientificImage acquisition & analysis YesYesYesYes
    (MicFac: neuron tracing)
    (Custom language)
    Volocity (Perkin Elmer) Scientific Image analysis (MicFac does not have acquisition license) YesYesYesYes
    (MicFac: deconvolution)
    MetaXpress (Molecular Devices) Scientific High-Content Image analysis Yes Yes Yes Yes Yes
    AcuityXpress (Molecular Devices) Scientific High-Content Database analysis use after MetaXpress analysis Moderate N/A Yes Yes Yes
    Scientific software, image analysis ONLY
    Fiji/ImageJ (NIH) Scientific Shareware Image analysis Yes Yes Yes Some Yes
    Arivis ScientificImage visualization (MicFac does not have analysis license)YesYesYes
    (MicFac does not have analysis license)
    (MicFac does not have analysis license)
    Imaris (Bitplane, MicFac copies) ScientificImage analysisYesYesYesYesYes
    (C, C++, MatLab)
    Imaris Viewer (Bitplane, free) ScientificImage analysisYesYes 3D View only No No
    MatLab (Mathworks) Scientific Image analysis (MicFac does not have acquisition license) ModerateYesYesYesYes
    Microvolution (Microvolution) Scientific High-speed (GPU) Deconvolution YesN/AN/AN/ASome
    Igor (WaveMetrics) Scientific Image analysis, AFM data ModerateYesYesYesYes

    Note: never use software to increase pixels/µm (increase image resolution). OK to reduce image resolution.

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