NIC 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).

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

• Spinning Disk Confocal
• TIRF/STORM
• Time Lapse
• 6D
• Spectral Confocal
• N-SIM
• High Speed Scope
• AZ100
• Other equipment and objectives

• Deconvolution Workstation 1 (older)
• Deconvolution Workstation 2 (newer)

• Accessing the NIC Server
• MyCores

• websites
• books
• presentations
• Microscopy Courses
• references
• NIC user guides
• Blogs

• Table of Fluorescent Proteins
• Interactive Graph of Fluorescent Proteins
• Dyes for 405 nm excitation
• Clearing methods
• Plates and dishes for imaging
• High Precision Coverslips
• Sample preparation for SIM imaging
• STORM sample preparation and imaging
• Protocol for ImmunoCytoChemistry in Cell Culture
• Calcium -FURA 2- imaging

• How to stich images acquired in Micro-Manager
• How to Acquire Flat Field correction images
• How to acquire color images with the RGB LED on the High Speed Microscope
• How to do background correction and large image stitching in ImageJ (OLD)

• 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.

• 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.

• Laser Cut and 3D Printed Parts for Microscopy
• PSFs and aberrations
• Consumables
• NIC PC Inventory