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
Data Analysis
How do I...
In MicroManager (at the scope)…
In Fiji/Image J…
📄 Brightness and Contrast Quick Tips
📄 Quick Channel and Look up Table tips
In other data analysis…
- Optical trap
- Deconvolution:
- Gradient Consensus by Andrew York - devolvement discussion on ImageJ Forum
- Huygens- Commercial software in core (also listed below)
Commercial Software available at the CALM
- NIS-Elements - Nikon’s image acquisition and analysis software. On NIC-Annalysis2 and 4 The same software we use to run most of the microscopes, this is also an easy-to-use tool for routine data analysis.
- Huygens - Huygens is a powerful and easy to use deconvolution program. On NIC-Annalysis4
- MATLAB - A popular commercial programming language and interactive environment for data analysis. Useful links to microscopy tools for Matlab are collected here.Note: this is available for all people at UCSF through and academic license from the school
Free Software
- ImageJ and Variants - One of the most commonly used free image analysis programs. Has a large and active development community.
- CellProfiler - A free, open source image analysis tool designed for analysis of image-based screens.
- Nikon Viewer - Free viewer for Nikon's file formats.
- 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.
- Use ilastik and cell profiler together! Check out the Cell Profiler and Ilastik: Superpowered segmentation blog entry and the How to use Pixel Classification in Cell Profiler, which has important instructions for the export of images from ilastik to get them into Cell Profiler!
GitHub sites
Fun Coding resources
-https://www.commands.sh/ - A searchable website for git, docker, shh comands.