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- ImageJ and Variants - One of the most commonly used free image analysis programs. Has a large and active development community.
- Nikon Viewer - Free viewer for Nikon's file formats.
- CellProfiler - A free, open source image analysis tool designed for analysis of image-based screens.
- Allen Cell Explorer - Resources from Allen Institute for Cell Science. Includes the Cell Feature Explorer, Cell Catalog, and Allen Cell Structure Segmenter.
- Napari - Multi-dimensional image viewer for python
- IOCBioMicroscope - A free, open source Lucy-Richardson deconvolution tool, written in Python.
- Farsight Toolkit - Sophisticated packages for image alignment, segmentation, and neuron / vessel tracing, among other things.
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