NeuroInfo Version History
NeuroInfo® Version 2025.1.1 (Latest Version)
Released November 2025
New Features and Enhancements
- New Map to Intermediate option is available after completing Section Registration using Atlas-constrained registration to create a brain image volume registration that can be further refined for better precision using the Register Volume tools
- New Nonlinear Registration options added provide better results and more control of the parameters used
- Calibration and transform information from image registration are now stored with the data file
- Additional tools and information in the Calibration panel:
- View information about installed atlases
- Atlas names now include the species, version, and section spacing
- Activate an updated or different brain atlas to modify the transforms from a previous registration
- 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
- Large image and data file handling are now faster and more robust
- Improvements and updates to the Movie mode interface have been implemented
- The Gerfen Nissl Mouse Atlas has been updated to version 2
NeuroInfo® Version 2024.1.3
Released December 2024
New Features and Enhancements
- Automove will now reposition focus when Continuous tracing is being used
- Improvements to synchronization of contours delineated in 2D and 3D
- Image file paths are displayed in the Image Organizer
- During a Movie, you can now change image-display settings for image slice and partial projections
- New ability to display the 3D scale bar while recording a Movie
- Other improvements and updates to the Movie mode interface have been implemented
NeuroInfo® Version 2024.1.1
Released August 2024
New Features and Enhancements
- Newly reimagined user interface to improve efficiency and usability of the section and volume registration processes
- New Atlas Constrained Section Registration improves anatomical region continuity throughout a serial sectioned brain
- Better integration with the Allen Mouse Brain Common Coordinate Framework (CCF) for improved registration and visualization of brain regions
- Improved Nonlinear registration algorithms
- 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 multi-image processing pipeline combine HDR image sets and filter expansion microscopy specimens to improve analyses
- Improvements to the movie tool make generating and viewing movies faster for large data sets and image volumes
- New “Go-to” buttons make it easy to apply listed transforms quickly
- Slide scans from MBF Bioscience image-acquisition systems can now be directly compiled in NeuroInfo
NeuroInfo® Version 2023.2.1
Released November 2023
New Features and Enhancements
- Added a new analysis tool for reporting experimental brain region volumes and intensities; these results can be exported to Excel
- In the Brain Region Ontology list, subregions can be automatically selected when the region is selected
- Markers can now be placed in the 3D visualization window
- Improved rendering and display responsiveness for millions of markers in 3D views
- Increased the speed of Map Experiment to Atlas for millions of markers from hours to minutes
NeuroInfo® Version 2023.1.1
Released May 2023
New Features and Enhancements
- Image registration (alignment) to a reference brain atlas has been completely re-engineered to include new Volume Registration tools and to make registration easier to use, more dynamic, and more robust. Highlights include:
- Using the new Register Volume process, you can align 3D volumes, either from intact, unsectioned tissue (e.g., cleared tissue) or blockface images, to a reference-brain atlas.
- Registering 3D serial-section reconstructions to an atlas using the Register Sections set of tools has been enhanced with updated registration algorithms
- Registration-integrated 3D visualization makes it easier to register experimental images to an atlas.
- Atlas calibration has been incorporated into the registration process, streamlining your work.
- New Map Atlas to Experiment tool, in combination with the updated Map Experiment to Atlas tool provides the capability to bidirectionally map experimental and atlas information.
- New ability to assign brain regions to the left or right hemisphere
- New ability to create and edit groups of anatomical structures of interest that can be used across experiments.
- Updated Waxholm rat-brain atlas included
- Faster Assemble Serial Sections (previously called the BrainMaker workflow) workflow processing to obtain 3D reconstructions from serial-section image sets.
- Nikon ND2 and Olympus VSI image formats are now supported
- Improved handling of multiple image formats, including CZI and some TIFF file types
- New Pipelines ribbon houses features previously located in the Automatic section of the Registration Ribbon
- New Batch Pipeline enables easy-to-use batch image filtering of multiple images—find it on the Pipelines ribbon
- In the Cell detection workflow, the image source is now automatically updated based on the image modality selected
NeuroInfo® Version 2022.1.1
Released April 2022
New Features and Enhancements
- Re-engineered BrainMaker workflow includes numerous enhancements, including a new Contact sheet that makes reordering sections easier
- Additional image formats are now supported
- Image selection will match between the BrainMaker workflow and the Image Organizer
NeuroInfo® Version 2021.1.4
Released September 2021
New Features and Enhancements
- Updated image processing and handling engines that greatly increase capabilities for image analysis and image loading and saving
- Section registration to atlases now includes a section-spacing constraint to improve the registration of brain volumes
- Additional AI classifiers are included
NeuroInfo® 2021.1.3
Released April 2021
New Features and Enhancements:
- Illumination correction that minimizes acquisition artifacts in fluorescent whole slide images
- New deep learning classifiers for detecting pyramidal cells
- Improved image loading, handling, and writing
- Reporting and saving average and summed intensities in brain regions
- Improved region editing in the 3D viewing window
- Clearer progress reporting and filter strength utilization in the cell detection workflow interface
- Faster and more stable connections to Biolucida slide servers from NeuroInfo
- Improved section detection in whole slide images
NeuroInfo® Version 2021.1.1
Released November 2020
New Features and Enhancements:
- Automated cell detection capabilities have been expanded
- Improvements to the speed and accuracy
- Now includes neural-network classifiers for intelligent identification and couting of specific neuronal subtypes
- A new, smart image background correction enables clear visualization and interpretation of compiled brain volumes
- New high-performance imaging engine that reads, renders, and writes big microscopy image and trace data that speeds up to 5000x faster than previous versions
NeuroInfo® Version 2020.1.1
Released November 2019
New Features and Enhancements:
- New interface and methodology for registering series of sections through whole mouse brains
- New technology for detecting cells in brain volumes and mapping cell coordinates to the Allen Atlas CCF for whole-brain screening of populations with objective anatomic specificity
- Added ability to use a single section to influence the registration of other sections from the same brain
- New tool for specifying cut orientation and spatial calibration correction for histological artifacts
- Automated installation of the latest mouse brain atlas from the Allen Institute
NeuroInfo® Version 2019.1.1
Released April 2019
New Features and Enhancements:
- Full specification of anatomic coordinates based on tissue cutting orientation
- Support for Huron, HDF5, and bigTiff formants
- Improved matching to the latest Allen Mouse Brain Atlas
- BrainMaker workflow included; ability to save as external XMP
- 3D automated cell detection improved speed and text number box included with the filter strength sliders
- 3D contour tracing added
- 3D marker placement added