SimuCell is an open-source framework for specifying and rendering realistic microscopy images containing diverse cell phenotypes, heterogeneous populations, microenvironmental dependencies and imaging artifacts. SimuCell can generate heterogeneous cellular populations composed of diverse cell types and allows users to specify interdependencies among population, biomarker and cell phenotypes
BioImageXD,written in Python and C++, is a free open source software project for analyzing, processing and visualizing of multi dimensional microscopy images.BioImageXD is a multi-purpose post-processing tool for bioimaging. The software can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.
CellProfiler is a free open-source software for high-throughput image-based cell profiling using fluorescence microscopy. It is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes.
The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets intended as a resource for testing and validating automated image-analysis algorithms. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth".
PhenoRipper is an open-source software tool designed for rapid exploration of high-content microscopy images that permits rapid and intuitive comparison of images obtained under different experimental conditions based on image phenotype similarity.PhenoRipper is designed to serve as an unsupervised exploratory tool for analysis of fluorescence microscopy images for both novices and experts.
CRImage is written in R and provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images. In particular, it allows cellularity scoring of tumours which can then be applied to correct molecular assay data for varying cellularity.
3D Visualization-Assisted Analysis (Vaa3D) is an open source cross-platform (Mac, Linux, and Windows) tool based on ITK libraries for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management.
The FARSight (Fluorescence Association Rules for multidimensional inSight) toolkit actively links scatter plots, histograms, dendrograms, bi-clustering panels with each other and with the multidimensional image data, enabling exploration of relationships among objects and among their derived numerical data. It also enables editing of segmentation and tracking results and quantitative analysis techniques, such as the automatic identification of outliers or groups among the features
μManager is a open source microscopy software package for control of automated microscopes. It mainly targets camera-based imaging, although it is also used with scanning systems. It includes an easy-to-use interface that runs as an ImageJ plug-in and enables researchers to design and execute common microscopy functions as well as customized image-acquisition routines.The program can be used to collect multichannel data over space and time, such as tracking fluorescently tagged cell fusion even
CISMM is one of several groups providing visualization and analysis tools freely usable by the biomedical microscopy community. There are a number of freely-available tools from other National Research Resources and elsewhere. We list some of them here for easy reference, along with brief descriptions
ScanImage provides a software framework to control laser-scanning microscopes and is used extensively for two-photon excitation microscopy. It implements most standard modes of image acquisition and basic automation, and supports continuous image acquisition synchronized to behavioral or physiological data, which is particularly useful for imaging in intact animals.
OMERO (Open Microscopy Environment Remote Objects) is an open-source client-server software platform that enables access to and use of a wide range of biological data. You can access your data in OMERO from any platform. By combining facilities for large-scale data management and a flexible, model-based architecture, OMERO provides a foundation for many different data-management challenges, especially where large, heterogeneous datasets must be accessed, viewed, analyzed and shared.
FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples.
Icy is a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows.It offers unique features for behavioral analysis, cell segmentation and cell tracking,
Fiji (Fiji is Just ImageJ) is an image processing package based on ImageJ and is currently the tool of choice in analysis of electron-
microscopy data.Fiji is effectively an open-source distribution of ImageJ that includes a great variety of organized libraries, plugins relevant for biological research
Ilastik (Interactive Learning and Segmentation Toolkit) is an open-source tool that enables researchers to train a machine-learning Random Forest classifier algorithm to identify which pixels of an image belong to which class of interest, based on the researcher providing example regions of each. Using it requires no experience in image processing.
ITK-SNAP is an interactive software application that allows users to navigate three-dimensional medical images, manually delineate anatomical regions of interest, and perform automatic image segmentation. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. Indeed, the main purpose is to make it easy for researchers to delineate anatomical structures and regions of interest in imaging data
Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)facilitates access to a growing number of neuroimaging tools and resources. Continuing to identify existing software tools and resources valuable to this community, NITRC’s goal is to support its researchers dedicated to enhancing, adopting, distributing, and contributing to the evolution of neuroimaging analysis tools and resources.