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Category: Biomedical images search, Imaging software
Broad Bioimage Benchmark Collection allows: Image database, Broad
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.
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Distributed trough GitHub
Category: Imaging software
CISMM allows: Image tools listing
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
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ImageJ from NIH is the most diffused public domain Java image processing program suitable for several scientific applications.
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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.
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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 (S. Rajaram et al., Nature Methods 9, 634, 2012).
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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.
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Category: Imaging software, Biomedical images search
OME | The Open Microscopy Environment allows: Image database
OME (Open Microscopy Environment) is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. It 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 OME 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-
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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.
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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.
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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
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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.
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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,
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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.
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protocols for 2D and 3D quantification in microscopic images
Category: Imaging software, Imaging tutorials
Microscopy-based imaging is booming and the need for tools to retrieve quantitative data from images is urgent. This book provides simple but reliable tools to generate valid quantitative gene expression data, at the mRNA, protein and activity level, from microscopic images in relation to structures in cells, tissues and organs in 2D and 3D. Volumes, areas, lengths and numbers of cells and tissues can be calculated and related to these gene expression data while preserving the 2D and 3D morpholo
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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.
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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
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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
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OsiriX is an open-source image processing software dedicated to DICOM images (".dcm" / ".DCM" extension) produced by imaging equipment (MRI, CT, PET, PET-CT, SPECT-CT, Ultrasounds, ...). It is available in 32-bit and 64-bit format and is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is at the same time a DICOM PACS workstation for imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D i
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EBImage provides general purpose functionality for high-throughput image processing and analysis in fluorescence microscopy. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data (Paut et
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Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy dataset (see Belevich et al., PLoS Biol. 14, e1002340 (2016).
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