Nutil

Nutil: Neuroscience Image Processing and Analysis Utilities

Nutil aims to simplify the pre-and-post processing of 2D brain section image data from mouse, rat and other small animal models. It can be used to preprocess images in preparation for analysis, and used as part of the QUINT workflow to perform spatial analysis of labelled features relative to a reference brain atlas. Nutil is developed as a stand-alone application with a simple user-interface, requiring little-to-no experience to execute.

Nutil currently supports four operations:

  • TiffCreater: convert images from JPEG, PNG and normal TIFF images to tiled TIFF format.
  • Transform: rename, rotate, resize and compile thumbnails of large tiled TIFF images (typical microscopy output).
  • Resize: resize JPEG/PNG images with output in PNG format.
  • Quantifier: perform quantification and spatial analysis of labelled features relative to a reference brain atlas (i.e. immunohistochemistry, in situ hybridization, tract tracing studies).

The following atlases are currently supported:

  • Allen Mouse Brain Atlas Common Coordinate Framework version 3 (2015 and 2017) (CCFv3)
  • Waxholm Atlas of the Sprague Dawley rat, version 2, 3 and 4 (WHS rat brain atlas).
Nutil
Launch online
Source Code
Contributors
JGB MAP SCY NG

Other Tools

See all tools

siibra-explorer

siibra-explorer is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometres.

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.

MeshView

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)

Create an account

EBRAINS is open and free. Sign up now for complete access to our tools and services.

Register