Curator Dashboard

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python package for downloading neurons morphological reconstructions from publicly available datasets. With the provided APIs, the user can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web interactive visualization tool of brain architecture based on tracer database.There are four modes of visualization: surfarce, flat, coronal, and saggital.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software high-throughput Mask R-CNN based toolbox to generate brain atlas through deep learning. Used for segmenting brain regions of interest.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software data pipeline which aligns histology images to the Allen CCF.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software visualization and analysis tool based on the Allen Brain Atlas connectivity database. Produces custom visualizations and figures for input output strength of specific brain area.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to map histological slice sequences to Allen Mouse Brain Atlas without 3D Reconstruction. Automatically maps histological slice to its corresponding plane in Allen Mouse Brain Atlas to build plane wise mapping and then perform 2D nonrigid registration to build pixel wise mapping.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Platform provides web interfaces for research institutions to exchange, share, and publish curated data and other digital resources.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools to split brain atlas regions and refine annotations accordingly. Applicable to the Allen Mouse Brain Atlas

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools to compute direction vectors in context of brain atlases.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software electrophysiology tool for planning Neuropixels recordings. Neuropixels trajectory planner for designing multi-probe insertions,utilizing the Allen Mouse Brain Common Coordinate Framework.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to test hypotheses about relation of patterns found in statistical maps with gene expression measured in postmortem brains. Refines corregistration coordinates provided by the Allen Institute.Used to compare statistical map of brain with gene expression patterns from Allen Human Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth