Cell Profiler
CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. See our papers on analyzing cell images and non-cell images

Cell Tracker
CellTracker is a free software environment for image browsing, processing and cell tracking. Using this software, you can track your targets in living cell imaging. It features:

  • Powerful and flexible image processing
  • Compact cell tracking wizard and flexible boundary tracking
  • Straight forward visualisation
  • Supports multiple export formats, including TIFF image, AVI video, spreadsheet and XML files

Image Surfer
ImageSurfer is free 3D imaging software to visualize and analyze multi-channel volumes (see Feng et al. 2007 ).
Features include:

  • Processing: 3D filters to improve signal-to-noise ratio.
  • Restoration: deconvolution algorithms (Wiener filter, Constrained iterative, Maximum likelihood).
  • Visualization: volume rendering, isosurface rendering, and a colored isosurface mode for qualitative display of the correspondence between two channels.
  • Analysis and quantification: 2D slice extractor, height field display, signal intensity sampling along user defined curves.

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and “raw”. It supports “stacks”, a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

The Microscopy Image Analysis Tool (MIATool) is a software application designed for the viewing and processing of large sets of image data. It makes efficient use of memory by working with pointers to images rather than the images themselves, and it saves disk space by storing reusable processing parameters in lieu of actual processed images on the hard drive. In addition, MIATool allows for multiple interpretations of a given image data set, realized by different, in general N-dimensional, arrangements of pointers to the images. A physical image data set can therefore be represented, viewed, and processed independently in different ways.

Sinema is a stand-alone program designed to automatically detect and track fluorescent particles in time-lapse image sequences. It is made and distributed to provide biologists and biophysicists with an easy-to-use tool for quantitatively analyzing data encountered in single molecule experiments.

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