Data Annotation and Segmentation Tools

ABAnnotate

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ABAnnotate is a Matlab-based toolbox that performs ensemble-based gene-category enrichment analysis (GCEA) on volumetric human neuroimaging data via brain-wide gene expression patterns derived from the Allen Human Brain Atlas. It utilizes a nonparametric method using spatial autocorrelation-corrected phenotype null maps for the estimation of gene-category null ensembles.

Atlas Alignment Meter 

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The Atlas Alignment Meter is a tool based in Python which can measure the slice-to-slice jaggedness of a volumetric dataset, only in the form of an NRRD file. 

Atlas Splitter

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The Atlas Splitter contains tools to split brain atlas regions and refine annotations accordingly, applicable to the Allen Mouse Brain Atlas.

Brainreg-segment

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The brainreg-segment tool works alongside the brainreg tool, allowing for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. 

CellLocator

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Cell Locator is an analysis tool that facilitates the manual alignment of tissue samples to common annotated 3D spaces. The user chooses a reference atlas of interest to then create and edit annotation files, and update the slice viewer plane orientation, thus localizing cell and tissue data in a consistent spatial framework.

SeBRe: Segmenting Brain Regions

Link  Relevant Publication 

SeBRe is a fully automated method for segmenting brain regions of interest. This is a Mask R-CNN-based toolbox created through deep learning. 

SMART: Semi-manual alignment to reference templates

Link Relevant Publication

SMART is an R package that builds a pipeline to process whole brain imaging datasets. This pipeline includes image registration, segmentation, coordinate navigation, standardized organization, and novel methods to parse through whole brain datasets and visualize data across various brain regions.

VoxHunt

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VoxHunt systematically compares single-cell transcriptomes to three-dimensional in situ hybridization (ISH) data to analyze brain organoid patterning, developmental state, and cell composition. 

Disclaimer

This list of third-party tools utilizing Allen Brain Map resources is for informational purposes only and do not constitute an endorsement or approval by Allen Institute of any of the tools or other products, services, or opinions of the associated organizations. Allen Institute bears no responsibility for the accuracy, legality, or content of the external tools or for that of subsequent links. The descriptions of these tools were adapted from their individual websites.