What's new

New features and improvements in NeuroInfo version 2025

  • You can now map the results of section registration to an intermediate brain space, then use the result to further refine the registration using the Register Volume tools.

    This new Map to Intermediate option is available after completing section registration using the Atlas-constrained method; it will create a brain image volume registration that can be further refined for better precision using the

  • New Nonlinear Registration options provide better results and more control of the parameters used. The new nonlinear registration tools are available for registering either sections or volumes. This method is particularly useful for samples that were distorted during processing or imaging.

  • Calibration and transform information from image registration are now stored with the data file

  • More tools and information for the Calibration used for registering images to a brain atlas:

    • You can view information about installed atlases

    • Atlas names in NeuroInfo now include the species, version, and section spacing

    • You can activate an updated or different brain atlas to modify the transforms from a previous registration. This may be very helpful for comparing results with different laboratories and online data repositories.

    • New warning if the atlas and/or spacing is not compatible with the experimental images

  • Improvements to the Tone Mapping filter

  • New marker density visualization surface option added to the 3D Visualization window that can help you see your data more clearly.

  • Large image and data file handling are now faster and more robust

  • Improvements and updates to the Movie mode interface have been implemented

  • The updated Gerfen Nissl Mouse Atlas (v2) is more clear and detailed than the previous version. We recommend using to this atlas version.

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

Previous releases

  • Update to offline software licensing. NeuroInfo software requires reactivation on systems that do not have access to the internet. View instructions for offline software activation.

  • 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.

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

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

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

  • 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

  • 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.