Curator Dashboard

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

Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas.Used to test for gene set expression enrichment in adult and developing human brain.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures. Identifies and defines relationships between four common atlases and characterizes their properties and organization. This model can serve as suggestion for minimum requiremens for atlases and will accelerate neuroscience data integration.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Allen Brain Atlas. Software toolkit to collect and preprocess expression data from Allen Brain Atlas and allow query to visualize spatial distribution of genes of interest, characterize spatial heterogeneity of brain, and register cells from single-cell transcriptomics data to fine anatomical brain regions via machine learning methods with high accuracy.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web based gene expression energy visualization tool.Created for visualizing expression energy data from the Allen Brain Atlas.ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to simplify process of producing graphics for expression data available in the Allen Institute's Brain Atlases. Related to Allen Mouse Brain Atlas.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software pipeline aiming at detecting transcripts enriched in hippocampal neuropil of adult mice, by systematically exploring high resolution images contained in Mouse Brain Atlas. Data mining tool that can provide information to select target genes whose nature will be studies and confirmed using biological tests.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Public research university with its main campus in Boca Raton, Florida and satellite campuses in Dania Beach, Davie, Fort Lauderdale, Jupiter, and Fort Pierce. The university is a member of the State University System of Florida.

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• RRID
• 3 years ago - submitted by Edyta Vieth

Private Jesuit research university in Omaha, Nebraska bridging health, law, business and arts and sciences for more just world.

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• RRID
• 3 years ago - submitted by Edyta Vieth

Provides instruments for performing widefield light microscopy, multiphoton microscopy, and confocal microscopy. Offers software for analyzing imaging data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides access to equipment to work on research projects, including cancer treatment research, vaccine development, and prosthetic creation. Instruments including micro-computed tomography (CT) scanner; scanning electron microscope (SEM); histology equipment; inverted fluorescence compound microscope; and stereoscope is available to FAU students (high school, undergraduate, graduate), post doctoral researchers, and faculty.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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• NIF
• 3 years ago - by Anonymous

Microscope enables super solution imaging of live cells at ten times the speed of conventional SIM. Powered by ECLIPSE Ti2-E Inverted Research Microscope, taking advantage of its advanced optics, stability and features.

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• RRID
• 3 years ago - by Anonymous

Arduino code, 3D print design files, and tutorial video on how to build LIQ HD system. Open source tool for recording undisturbed two-bottle drinking behavior in home cage environment. All designs and software are open source to allow other researchers to build on the system and adapt LIQ HD to their animal home cages.

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• RRID
• 3 years ago - submitted by Jensen Palmer

Web tool for functional analysis of sets of miRNAs. Tailored for miRNA precursors and mature miRNAs of multiple frequently investigated species. Used for miRNA set enrichment analysis. miEAA 2.0 is updated version for integrating multi-species microRNA enrichment analysis and workflow management systems.

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• RRID
• 3 years ago - by Anonymous