What's new

See the current Release Notes or all Release Notes for NeuroInfo.

• Redesigned interfaces for Register volume and Register sections improve the efficiency and usability of powerful NeuroInfotools for registering experimental brain images to publicly available brain atlases

• Serial Section Assembler is the new name for the Brainmaker workflow, that enables you to generate high-resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes.

• New atlas-constrained section registration provides improved anatomical-region continuity throughout a serial sectioned brain

• New “Go-to” buttons make it easy to navigate to and apply established transforms quickly

• Better integration with the Allen Mouse Brain Common Coordinate Framework (CCF) for improved registration and visualization of brain regions

• Improved nonlinear transformation algorithms for both Register volume and Register sections can improve registration to account for variation between individuals and some deformations introduced by processing.

• New Analysis tool calculates and displays quantitative information about brain regions identified in your images. Includes number of markers, volume, and average pixel intensity per region.

• Three-dimensional visualization can now eliminate edge artifacts at the surfaces of brain volumes

• Image montage tool assembles overlapping fields of view while minimizing seaming artifacts and uneven illumination

• New image filters in our Batch pipeline combine HDR image sets and filter expansion microscopy specimens to improve analyses

• Improvements to the movie tool in the 3D Visualization window make generating and viewing movies faster for large data sets and image volumes

• Slide scans from MBF Bioscience image-acquisition systems can now be directly compiled in NeuroInfo

Previous releases

• In the Brain Region Ontology list, the new Include sub-regions with selection checkbox enables sub-regions to be automatically selected when the main region is selected.

• Added the ability to place markers in the 3D visualization window.

• Rendering and display responsiveness has been improved for millions of markers in the 3D views.

• The speed of Map Experiment to Atlas for millions of markers has been increased to take minutes instead of hours to complete.

• Serial Section Assembler is the new name for the Brainmaker workflow, that enables you to generate high-resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes. It includes numerous enhancements, including a new Contact sheet that makes reordering sections easier

• Image registration (alignment) to a reference brain atlas has been re-engineered to include new Register volume tools and to make Register sections easier to use, more dynamic, and more robust.

• The cell detection workflow interface now has improved progress reporting and filter strength utilization; it also includes new classifiers for cell detection that employ deep learning

• New Batch Pipeline enables easy-to-use batch image filtering of multiple images

• New Pipelines ribbon houses features previously located in the Automatic section of the Registration ribbon

• Improved handling of multiple image formats, including CZI, some TIFF file types, Nikon ND2, and Olympus VSI image formats.

• Updated image processing and image handling engines that greatly increase capabilities for image analysis and image loading and saving.

• Individual color channels can now be displayed using gradient color maps that make it significantly easier to see features in many cases.

• Average and summed image intensities in regions throughout brain volumes can now be reported and saved