UCSF CALM Microscopy Wiki
UCSF CALM Microscopy Wiki
Wiki
View the Project on GitHub
UCSF-CALM/wiki
Contents:
- Home
- Microscopes
- Spinning Disk Confocal
- TIRF/N-STORM
- Time Lapse
- 6D
- Crest LFOV/C2
- CSU-W1
- AZ100 Light Sheet
- OMX-SR
- TruLive3D Light Sheet
- C-Trap Optical Tweezers
- QLIPP Timelapse with Nanoindentor
- Snouty Light Sheet
- CVRI Nikon Spinning Disk
- CVRI Nikon Spinning Disk
- CVRI Leica SPE Confocal
- Other Equipment and Objectives
- Data Analysis Workstations
- Data Analysis
- Sample Preparation
- References & Education
- CALM Information
- Miscellaneous
Contents:
- Home
- Microscopes
- Spinning Disk Confocal
- TIRF/N-STORM
- Time Lapse
- 6D
- Crest LFOV/C2
- CSU-W1
- AZ100 Light Sheet
- OMX-SR
- TruLive3D Light Sheet
- C-Trap Optical Tweezers
- QLIPP Timelapse with Nanoindentor
- Snouty Light Sheet
- CVRI Nikon Spinning Disk
- CVRI Nikon Spinning Disk
- CVRI Leica SPE Confocal
- Other Equipment and Objectives
- Data Analysis Workstations
- Data Analysis
- Sample Preparation
- References & Education
- CALM Information
- Miscellaneous
Books, Websites, Etc
Microscopy References and Education
General Microscopy
Michael Davidson maintains an excellent family of websites, many sponsored by manufacturers, which are an excellent source of microscopy information:
- Molecular Expressions
- Nikon Microscopy U
- Zeiss MicroImaging Campus
- Olympus Microscopy Resource Center
- Hamamatsu Learning Center
Specific Microscopy/Optics Resources
Fluorescent Probes
- The Molecular Probes Handbook - a good source of information on fluorescent dyes and small molecule reporters.
- openoptogenetics - Optogenetics wiki site with good technical information.
- FPbase - a good source of information on fluorescent proteins. Spectra viewer also useful for comparison of filter sets between different fluorescent proteins.
Data Analysis
- John Maloney has a very nice presentation on statistics and data analysis from the MIT IAP: Maloney.pdf
- A nice primer on image analysis in ImageJ/Fiji: Analyzing fluorescence microscopy images
- Peter Bankhead’s Analyzing Fluorescence Microscopy Images with ImageJ gitbook
- Ljosa V, Carpenter AE. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. PLoS Comput Biol. 2009 Dec;5(12):e1000603.
- Basics of Quantitative Image Analysis (large slide set with good illustrations of important analysis concepts)
- Jim Pawley. The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy. Biotechniques. 2000 May;28(5):884-6, 888.
- Jennifer C. Waters. Accuracy and precision in quantitative fluorescence microscopy. Journal of Cell Biology 2009 185(7):1135-1148.
- Douglas W. Cromey. Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images. Sci Eng Ethics (2010) 16:639-667.
Blogs
- Brain Windows - A neuroscience postdoc’s posts, focused on brain imaging.
- Austin Blanco’s Microscopy blog - From one of Technical Instrument’s former employees.
- Labrigger - Blog that offers alternatives to expensive lab equipment.
- Kurt’s Microscopy Blog - From the director of the NIC.
Forums
- Image.sc - Community forum for multiple open-source image analysis software packages where you can find answers to common problems and post questions to the community. The forum is very active and you can get help quickly.
- Microforum - Community forum based on hardware, acquisition, and specimen-related questions.
Miscellany
Recommended Books on Microscopy
Fundamentals of Light Microscopy and Electronic Imaging, Douglas B. Murphy: A good general purpose introduction to commonly used microscopy techniques, including fluorescence, phase contrast and DIC, and brief discussions of confocal microscopy and cameras.
Handbook of Biological Confocal Microscopy, 3rd ed., James Pawley, ed.: This is the book to get if you want an in-depth understanding of not just confocal microscopy, but the whole diversity of modern microscopy techniques. It’s not a good introduction to the subject but it is a fantastic reference work with lots and lots of technical detail.