Windows

GelBandFitter is a user-friendly software specific for analysis of protein gels and estimation of relative protein content. Using non-linear regression methods to fit mathematical functions to densitometry profiles, it is able to estimate content from protein bands that partially overlap. The software is available either as Matlab code (Optimization toolbox required) or a Windows executable. Reference: Mitov, M. I., Greaser, M. L., & Campbell, K. S. (2009). GelBandFitter – A computer program for analysis of closely spaced electrophoretic and immunoblotted bands. Electrophoresis, 30(5), 848–851. http://doi.org/10.1002/elps.200800583

SRRF is a high-performance analytical approach for Live-cell Super-Resolution Microscopy, provided as a fast GPU-enabled ImageJ plugin. SRRF is capable of extracting high-fidelity super-resolution information from TIRF, widefield and confocals using conventional fluorophores such as GFP. SRRF is capable of live-cell imaging over timescales ranging from minutes to hours.

Spotsizer is a software tool that automates analysis of large volumes of photographic images of growing microbes.

CellProfiler is free, open-source software for quantitative analysis of biological images.

CellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure cell or whole-organism phenotypes from thousands of images automatically. The researcher creates an analysis pipeline from modules that find cells and cell compartments, measure features of those cells to form a rich, quantitative dataset that characterizes the imaged site in all of its heterogeneity. CellProfiler is structured so that the most general and successful methods and strategies are the ones that are automatically suggested, but the user can override these defaults and pull from many of the basic algorithms and techniques of image analysis to solve harder problems. CellProfiler is extensible through plugins written in Python or for ImageJ. Strengths: Cells, Neurons, C. Elegans, 2D Fluorescent images, high-throughput screening, phenotype classification, multiple stains/site, interoperability, extensibility, machine learning, segmentation Limitations: largely limited to 2D, not well suited to manually-guided analysis or content review, image size limitations

PopulationProfiler – is light-weight cross-platform open-source tool for data analysis in image-based screening experiments. The main idea is to reduce per-cell measurements to per-well distributions, each represented by a histogram. These can be optionally further reduced to sub-type counts based on gating (setting bin ranges) of known control distributions and local adjustments to histogram shape. Such analysis is necessary in a wide variety of applications, e.g. DNA damage assessment using foci intensity distributions, assessment of cell type specific markers, and cell cycle analysis.