QuickNII
Software for 2D image registration to 3D atlas.
Brain atlasesData integration
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).
Other software
All softwareVisuAlign
Software for 2D image registration to 3D atlas.
Brain atlasesData integration
ilastik
Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.
Data analysis and visualisationBrain atlases