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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/qiicr/dcmqi
Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.
Proper citation: dcmqi (RRID:SCR_016933) Copy
https://github.com/QTIM-Lab/DeepNeuro
Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.
Proper citation: DeepNeuro (RRID:SCR_016911) Copy
A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.
Proper citation: 3D Slicer (RRID:SCR_005619) Copy
Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium.
Proper citation: Harvard Medical School Center for Cancer Systems Pharmacology (RRID:SCR_022831) Copy
https://kleintools.hms.harvard.edu/tools/spring.html
Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data.
Proper citation: SPRING (RRID:SCR_023578) Copy
Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases.
Proper citation: Minerva (RRID:SCR_024750) Copy
Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells.
Proper citation: scimap (RRID:SCR_024751) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
