Curator Dashboard

Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools to work with Allen Inst CCF data in Matlab. MATLAB code to work with the Allen Mouse Brain CCF data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for assessing brain organoid patterning, developmental state, and cell composition through systematic comparisons of single cell transcriptomes to three-dimensional in situ hybridization data from the Allen Brain Atlas and number of other useful reference datasets.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool analyzes single-cell RNA-seq dataset from the Allen Mouse Brain Atlas to isolate the analysis of hierarchical structure and the discovery of important genes in the mouse neocortex.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Respository contains two small software tools which render annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial).

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software provides visualization and slicing of 3D isotropic image data as well as various atlases. Through orthogonal views of three standard planes (coronal, sagittal, horizontal) and custom-angle slice cut through the volume, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles. Custom slicing then allows for the inspection of anatomical features from non-conventional angles.Custom-angle slicer for brain atlas volumes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python package utilizes spatial, anatomical, microarray expression data from the Allen Institute for Brain Science. This program maps genes of interest (Goi) by their levels of expression to brain regions (Roi). The identified regions that co-express the input Goi can, in turn, be studied further with many experimental modalities. This program can be customized to map gene expression data and identify significant Roi from similar reference expression data in other contexts outside of neuroscience.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to simplify creation of procedural meshes. Used to generate separate mesh files for each label present in segmentation volume, simplifying creations of procedural meshes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software atlas based imaging data analysis tool for quantitative mouse brain histology. Can automatically detect cells in histological mouse brain and spinal cord sections of interest.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package to the infer spatial location of neural progenitor subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth