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 MicFac Members to use. 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)	Class	Purpose	Ease-of-use	Basic Adjust-ments	Basic Analysis	Advanced Analysis	Programmability
  Photo software (not scientific; professional/consumer grade)
  Illustrator (Adobe)	Pro-sumer	Vector-based drawing; Image layout; Submission of composite images for publication	Moderate	Yes	No	No	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
  AxioVision (Zeiss)	Scientific	Image acquisition & analysis	Yes	Yes	Yes	Some (MicFac: deconvolution)	No
  Slidebook (3i)	Scientific	Image acquisition & analysis	Yes	Yes	Yes	Some (MicFac: deconvolution)	No (indirect with MatLab)
  Metamorph (??)	Scientific	Image acquisition & analysis	Yes	Yes	Yes	Yes (MicFac: neuron tracing)	Yes (Custom language)
  Volocity (??)	Scientific	Image analysis (MicFac does not have acquisition license)	Yes	Yes	Yes	Yes (MicFac: deconvolution)	Graphical
  Scientific software, image analysis ONLY
  ImageJ (NIH)	Scientific Shareware	Image analysis	Yes	Yes	Yes	Some	Yes (Java)
  Imaris (Bitplane)	Scientific	Image analysis	Yes	Yes	Yes	Yes	Yes (C, C++, MatLab)
  MatLab (Mathworks)	Scientific	Image analysis (MicFac does not have acquisition license)	Moderate	Yes	Yes	Yes	Yes
  Igor (??)	Scientific	Image analysis	Moderate	Yes	Yes	Yes	Yes

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