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Aphelion

A commercial image analysis software.
It's interface allows to easily perform measurements and image analysis. Your actions can be recorded and a macro (in a basic script language) can then be created. Almost no knowledge in programming is needed. You can also use python.
A SDK is also available to develop stand alone applications in c++.
Additional modules allow to use specific operations (3D operators...

dscho's picture

Imaris

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

dscho's picture

FARSIGHT

A General purpose image processing toolkit written in C++ based on ITK, VTK, Qt, and Boost. Main features: algorithms for cell segmentation, cell tracing, cell tracking, and vessel tracing. Registration and mosaicing algorithms for large scale datasets. Visualization tools actively linked to inspect and edit results.
Strengths:
- Open-source, free, multi platform, code is highly parallelized, uses git for version control
- Large scale processing, also efficient visualization of such datasets.
- Active learning module for classification

dscho's picture

Icy

Reproducing an experiment doesn’t stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team.

dscho's picture

CellProfiler

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.

Ofra Golani's picture

WIS-NeuroMath

WIS-NeuroMath - is a software tool for automated analysis and quantification of fluorescent microscopy images of Nerve cells, in both in vivo and in vitro preparations. It allows for accurate detection of neurites in challenging images. Following neurite detection, different types of processing can be carried: Cell Morphology of cultured neurons, Neurite Length Analysis and Ganglion Explant Analysis.
Usefull also for angiogenesis analysis.

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ExportToDatabase

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ExportToSpreadsheet

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