What's new

• 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.

• 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.

• 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. Highlights of the changes include the following:

  • Using the new Register volume process, you can align 3D image volumes obtained from intact, unsectioned tissue specimens (e.g., cleared tissue) or blockface images to a reference-brain atlas to identify brain regions.

  • Registering 3D serial-section reconstructions to an atlas using the Register sections tool set has also been improved with updated registration algorithms.

  • 3D visualization is now integrated in the Section and Volume registration tool sets, making it easier to register experimental images to an atlas.

  • Atlas calibration has been incorporated into the registration process for registering from assembled sections and intact image volumes.

  • Brain regions can now be assigned to the left or right hemisphere.

  • Added the ability to create and edit groups of anatomical structures of interest that can be used across experiments.

  • New Map Atlas to Experiment tool, in combination with the legacy Map Experiment to Atlas tool provides the option to bidirectionally map experimental and atlas information.

  • Use the Map Experiment to Atlas tool to map experimental data, such as markers and 2D contours, into the common reference space of the reference brain atlas, so that you can make quantitative comparisons between individual brains and share data across different research teams and laboratories.

  • Updated Waxholm rat-brain atlas available for download on the MBF Bioscience Download Center.

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

Previous releases

• In the Cell detection workflow, the image source is now automatically updated based on the image modality selected.

• 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 and some TIFF file types.

• Nikon ND2 and Olympus VSI image formats are now supported.

• Re-engineered Serial Section Assembler (formerly BrainMaker workflow) includes numerous enhancements, including a new Contact sheet in the that makes reordering sections easier

• 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.

• The cell detection workflow interface now has improved progress reporting and filter strength utilization

• New classifiers for cell detection that employ deep learning have been added

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