Freeware for Analysis

Optical Imaging Core

Useful Resources

Analysis and Processing Software (free or open-source)

Image manipulation and analysis


FIJI is Java-based software for working with image data and is available for all operating systems. Its plug-ins cover an extensive range of imaging needs, including:

  • Manipulation of images, time lapse, Z stacks and color
  • Annotation, including scale and time
  • 3-D modeling and visualization
  • Quantitative analysis of image properties such as intensity, particle measurement and tracking, colocalization etc.

FIJI is used and maintained by an extensive range of imaging scientists and professionals.


GIMP is a free and powerful alternative to Adobe Photoshop with versions available for most operating systems.

Matlab packages from the Danuser lab

  • uTrack 2.0: Sophisticated particle tracking algorithm
  • Biosensor Processing: Automated analysis and generation of heat maps from ratiometric biosensor data
  • QFSM: Speckle analysis of actin, tubulin polymerization
  • cmeAnalysis: Quantifies clathrin-coated pit dynamics from time-lapse data
  • plusTipTracker: Tracks many microtubule parameters using +TIP marker live cell imaging
  • ClusterTrack: Works with plusTipTracker to allow analysis of microtubules using only +TIP imaging
High throughput analysis


CellProfiler is a machine learning-based tool for automated and quantitative analysis of high-throughput data sets (e.g., high volume fluorescent phenotype screens). It is very good at segmentation (nucleus, PM, cytoplasm) of cells in culture and tissues.


CellClassifier is a machine-learning tool for automatically classifying cells into custom categories and measuring their properties. It is based on CellProfiler and requires the Statistical Pattern Recognition Toolbox for Matlab.


Endrov is an open-source image analysis system and an alternative to Fiji and CellProfiler.

3-D visualization and analysis

ImageSurfer, ImageSurfer2

ImageSurfer and ImageSurfer2 can be used for the visualization and manipulation of 3-D data sets. Additionally, ImageSurfer allows for deconvolution using a recorded PSF (functionality is pending in ImageSurfer2).


MorphoGraphX allows for the visualization and manipulation of 3-D data sets. It requires an nVidia 3-D graphics card with suitable RAM.


Vaa3D allows for the visualization and manipulation of 3-D and 4-D data sets. It also allows the use of TeraStitcher.

Data management


Bio-Formats is a standalone program that opens most proprietary image formats (e.g., Nikon .nd2, Zeiss .lsm etc) and allows them to be saved in a common format (e.g., TIFF). It integrates as a plug-in with free image processing apps such as Fiji, CellProfiler, etc.


OMERO is a program for managing and manipulating large collections of image data and is comparable to Adobe Lightroom. It integrates as a plug-in with free image processing apps such as Fiji, CellProfiler, etc.


Micro-Manager was designed for the control of automated microscopes and is comparable with Metamorph.

Resolution enhancement

Bayesian analysis of blinking and bleaching (3B)

This free, open source software provides a processing step after repeated laser imaging. This allows for higher resolution images using standard labels and illumination methods.

Photobleaching with nonlinear processing

This technique allows for algorithmic analysis of bleaching during continuous imaging. No special equipment is required.


Superresolved.com provides information about super-resolution microscopy techniques, including options that can be accomplished with standard imaging tools and free software.