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Nikon Imaging Center at UCSF / QB3 Wiki

This wiki will be used for general information about microscopy and microscopy-related science and technology that may be of interest to both the UCSF community and the broader microscopy community. If you would like to contribute to the wiki, please email kurt.thorn@ucsf.edu to get an account (we have disabled signups due to spam).

Nikon Imaging Center Microscopes

Here is a repository for information about the NIC microscopes, including technical details and information for end users.

Data Analysis Workstations

Other NIC Information

Microscopy References and Education

Sample Preparation

Data Analysis

Protocols
Commercial Software available at the NIC
  • 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.
Free Software
  • ImageJ and Variants - One of the most commonly used free image analysis programs. Has a large and active development community.
  • Nikon Viewers - Free viewers for Nikon's file formats.
  • CellProfiler - A free, open source image analysis tool designed for analysis of image-based screens.
  • IOCBioMicroscope - A free, open source Lucy-Richardson deconvolution tool, written in Python.
  • python(x,y) - A complete python package, including libraries and IDE, for scientific computing.
  • Farsight Toolikit - Sophisticated packages for image alignment, segmentation, and neuron / vessel tracing, among other things.

Miscellaneous

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