NeuroInfo Glossary

Following are definitions of words that be unfamiliar to you, with a focus on how they are used in NeuroInfo software.

Brain atlas: A brain reference map showing anatomic structures and in some cases other information such as connectivity or function. Atlases are often used to identify parts of the brain or compare information derived from experiments conducted in different ways and in different laboratories. Within NeuroInfo, a brain atlas comprises a reference image used for registration, a segmentation of this image into different anatomic regions, and the hierarchical relationship among brain regions. The brain atlas used in registration of experimental sample images

Select the reference brain atlas that you want to use in NeuroInfo when you specify or create the calibration to use for section registration or volume registration of your experimental brain.

The following brain atlases are formatted and available for use in NeuroInfo; the Mouse Allen/MBF CCF v3 25um (coronal orientation) and the Mouse Gerfen/MBF v2 Nissl 25um are installed with the NeuroInfo installer. The other atlases can be downloaded from the MBF Bioscience download center (see instructions for installing brain atlases).

  • Mouse Allen CCFv3: The Allen Mouse Brain Common Coordinate Framework (CCF) version 3, was created by the Allen Institute for Brain Science to support large-scale collaborations that include comprehensive surveys of cell types and connections in the mouse brain, and large amounts of data across modalities, spatial scales, and brain areas. Its creation is described in Wang, Quanxin et al., The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas, Cell, Volume 181, Issue 4, 936 - 953.e20.

    The Allen adult mouse CCFv3 in the sagittal orientation is available at 10 µm and 25 µm primary voxel spacing. These atlases can be downloaded from the MBF Bioscience download center (see instructions for installing brain atlases)

    After installation, the Mouse Allen CCFv3 atlases appear as follows in the Atlas dropdown menu in NeuroInfo, :

    • Mouse Allen CCFv3 10um: Allen Institute for Brain Science, Mouse Brain Atlas CCFv3 2017, sagittal orientation, 10um

    • Mouse Allen CCFv3 25um: Allen Institute for Brain Science, Mouse Brain Atlas CCFv3 2017, sagittal orientation, 25um

  • Mouse Allen/MBF CCFv3: A version of the Allen Mouse Brain CCF v3 modified by MBF Bioscience from the sagittal to the coronal orientation. This atlas has been included in NeuroInfo software since its release; it was formerly called "AllenCCF Default".

    This atlas is available at 10 µm and 25 µm primary voxel spacing. In NeuroInfo, these will appear as follows in the Atlas dropdown menu:

    • Mouse Allen/MBF CCFv3 10um (available on the MBF Bioscience download center): Allen Institute for Brain Science, Mouse Brain Atlas CCFv3 2017, coronal orientation modification, 10um

    • Mouse Allen/MBF CCFv3 25um (included in the NeuroInfo software installer): Allen Institute for Brain Science, Mouse Brain Atlas CCFv3 2017, coronal orientation modification, 25um

  • Mouse Gerfen/MBFv2: Adult mouse brain atlases developed by Charles Gerfen (NIMH) in collaboration with MBF Bioscience from multiple mouse brains imaged by sectioning, Nissl-staining, and reconstruction using the NeuroInfo Serial Section Assembler. There are two versions of the atlas and v2 is available at 10 µm and 25 µm primary voxel spacing. In NeuroInfo, these atlases appear as follows in the Atlas dropdown menu:

    • Mouse Gerfen/MBF V1 Nissl 16um (formerly called GerfenNissl2017, available on the MBF Bioscience download center): the original fluorescence Nissl-stained brain developed in collaboration with Dr. Chip Gerfen

    • Mouse Gerfen/MBF V2 Nissl 25um (included in the NeuroInfo software installer): 25 µm primary voxel spaced version of the updated Gerfen Nissl average brain that comprises 80 new brains. This atlas is co-registered to the Mouse Allen/MBF CCFv3 (the MBF Bioscience-modified coronal version ) and has a much higher level of detail than the original.

    • Mouse Gerfen/MBF V2 Nissl 10um (available on the MBF Bioscience download center): 10 µm primary voxel spaced version of the updated Gerfen Nissl atlas

  • Waxholm Rat Atlases: The Waxholm Space rat brain atlas is a comprehensive open-access volumetric rat brain atlas, covering all major systems of the brain with detailed annotations. The atlas is based on an isotropic, high-resolution, contrast-enhanced sMRI/DTI dataset acquired ex vivo from an adult male Sprague Dawley rat brain and is described in this publication.Two variations of the Waxholm rat atlas are available to download from the MBF Bioscience download center; they appear as follows in the Atlas dropdown menu:

    • Rat Waxholm V4 39um: Version with the "skull-stripped" MRI reference image, meaning that the non-brain tissue is removed from the reference image.

    • Rat Waxholm V4 39um (spine strip): Version with several additional anatomic regions stripped from the reference image so that they do not influence registration:spinal cord (45), spinal trigeminal tract (76), optic nerve (41). Note that these regions are available in the ontology and anatomy images and can be visualized.

Calibration: A NeuroInfo calibration captures basic information about an experimental image, including its anatomic orientation, the atlas to which it will be registered, and its approximate scale relative to the atlas. In Volume Registration, the calibration also includes the approximate optical sectioning angle. The same calibration can be used for many experimental images that are prepared in the same manner. Starting with NeuroInfo version 2025, the calibration used for registration is saved with the data file created when brain images are registered to an atlas.

Experiment image: In NeuroInfo, this refers to a digital, microscopy image of a brain section or brain-image volume. This can come from many sources, for example serial section reconstructions of whole slide images, block-face imaging, or image acquisition from intact tissue (e.g., cleared tissue).

Intact image volume: a 3D microscopy image that represents a part or whole brain imaged without physical sectioning, for example from light-sheet microscopy of cleared tissue.

Physical coordinate space: defines the physical properties of an image in real-world units. This establishes a physical representation of the pixel coordinates of an image: the origin, spacing between pixels, and direction of the image axes.

Reference Section: A key section of the experimental image that has been interactively registered to a brain atlas. Reference sections typically have prominent anatomic features that make them suitable for interactive review to ensure accuracy. Reference sections are used in serial section registration to initialize the registration of other sections in the brain.

Registration: a process that finds the geometric mapping between the physical coordinate spaces of the experiment image and the atlas. Registration produces a transform that maps points in the experiment image onto corresponding points in the atlas, effectively aligning comparable images to each other.

The following categories of registration can be applied to serial section images using the NeuroInfo Section Registration tools:

  • Single section registration: Each section has a completely independent transform

  • Serial section, Independent registration: Each section has an independent transform with some fixed parameters

  • Atlas-constrained registration:Each section has a transform with some independent parameters and some shared parameters. This method is recommended if all sections are evenly spaced.

For images of unsectioned specimens or intact image volumes, a single transform is applied to the whole volume using NeuroInfo Volume Registration process.

NeuroInfo can create The following are different types of transforms used in :

Linear Transformation:applies the same operation everywhere in space (e.g., translation, rotation, and scaling. In many cases, we recommend running linear transformation first. The exception is when the experimental sample was deformed during processing or imaging.

Nonlinear Transformation: Nonlinear transformation optimizes a transform that is defined by a grid of parameters that are spatially aligned to the experimental image. It applies different operations in different parts of space (e.g., local deformation or warping).

Nonlinear transformation may be especially helpful for brain images from samples that were deformed during processing or imaging.

Serial Section Reconstruction: a series of histologic section images that have been assembled into a 3D image volume representing the pre-sectioned brain, for example with the Serial Section Assembler.

Transform: A transform maps geometric points from one physical coordinate space into another. NeuroInfo creates one or more transforms as the result of registering a brain image or series of brain-section images to a brain atlas. Transforms record the alterations in the size, shape, and/or sectioning angle of the reference atlas needed to register (align) the experimental brain image to the atlas.

When using NeuroInfo Section Registration, a transform is generated for each section; Volume Registration on the other hand generates a single transform.

Transform Set: a collection of transforms, one for each section in a serial section registration. Transform Sets are not relevant for image-volume registration.

When registering multiple sections, save sets of transforms in separate folders to avoid overwriting or mixing results from different animals or registration attempts.