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Protocols
Commercial Software available at the CALM
- NIS-Elements - Nikon's image acquisition and analysis software. The same software we use to run most of the microscopes, this is also an easy-to-use tool for routine data analysis.
- MetaMorph - Another program for interactive data analysis.
- MATLAB - A popular commercial programming language and interactive environment for data analysis. Useful links to microscopy tools for Matlab are collected here.
- Huygens - Huygens is a powerful and easy to use deconvolution program.
- Slidebook - 3i commercial software package for image acquisition and analysis.
Free Software
- 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.
- Ilastik- Machine learning algorithms to segment, classify, track and count your cells or other experimental data.
GitHub sites
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