Analysis and Processing Software (free or open-source)
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:
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.
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.
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.
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.
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.
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.