Semi-automated

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

BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.

Advanced Cell Classifier is a data analyzer program to evaluate cell-based high-content screens and tissue section images developed at the Biological Research Centre, Szeged and FIMM, Helsinki (formerly at ETH Zurich). The basic aim is to provide a very accurate analysis with minimal user interaction using advanced machine learning methods.

A standalone cell tracking software for single cell migration. Tracking of cells in tissue was also done in Drosophila germband.

The ImageJFX Project aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While keeping the core components of ImageJ, ImageJFX brings scientists closer to their goal by making the interface clearer for beginners and more practical for advanced users.