ImageJ

ImageJ is an open source image processing program designed for scientific multidimensional images. ImageJ is highly extensible, with thousands of plugins and scripts for performing a wide variety of tasks, and a large user community.

  • Open source: ImageJ is a tool for the scientific community. To maintain transparency, the ImageJ application and its source code will always be freely available.
  • Reproducible: Powerful tools such as the Script Editor and personal update sites help you develop and share reproducible analysis workflows.
  • Interoperable: ImageJ is not an island. Use the best tool for the job, including KNIME, ITK, MATLAB, and a multitude of scripting languages.
Launch online
Source Code
Contributors
RL AF GH BD AG JS LK MH BN CD CR WR

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Collaboratory

The EBRAINS Collaboratory offers researchers and developers a secure environment to work with others. You control the level of collaboration by sharing your projects with specific users, teams or all of the Internet. Many researchers are sharing their work already; several services, tools, datasets and other resources are publicly available, and many more are available for registered users.

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MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain. MeshView is available as an EBRAINS community app, accessible via a collab (further info: https://wiki.ebrains.eu/bin/view/Collabs/image-registration-and-analysis-demo/) Key features: orbiting view with toggleable opaque/transparent/hidden parcellation meshes rendering user defined cut surface as if meshes were solid objects rendering point-clouds (simple type-in, or loaded from a JSON format) coordinate system is compatible with QuickNII (https://www.nitrc.org/projects/quicknii)

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