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http://purl.bioontology.org/ontology/ABA-AMB
Allen Brain Atlas P56 Mouse Ontology
Proper citation: ABA Adult Mouse Brain Ontology (RRID:SCR_010286) Copy
http://casestudies.brain-map.org/celltax
Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.
Proper citation: CellTax vignette (RRID:SCR_017000) Copy
The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.
Proper citation: Aging Dementia and Traumatic Brain Injury Study (RRID:SCR_014554) Copy
http://www.informatics.jax.org/home/recombinase
Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.
Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) Copy
3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.
Proper citation: Allen Mouse Brain Common Coordinate Framework (RRID:SCR_020999) Copy
https://www.mozak.science/landing
Scientific discovery game about neuroscience that helps to build models of brain cells.
Proper citation: Mozak (RRID:SCR_021008) Copy
https://sagebionetworks.org/portals/
Platform provides web interfaces for research institutions to exchange, share, and publish curated data and other digital resources.
Proper citation: SageBionetworks Portals (RRID:SCR_023844) Copy
https://biop.github.io/ijp-imagetoatlas/
Software Fiji plugin for registering thin serial sections: coronal, sagittal, horizontal, to compatible atlases including Allen Mouse Common Coordinate Framework, Waxholm Rat Brain Atlas, and all BrainGlobe atlases.
Proper citation: Aligning Big Brains and Atlases (RRID:SCR_023857) Copy
https://github.com/VirtualBrainLab/Pinpoint
Software electrophysiology tool for planning Neuropixels recordings. Neuropixels trajectory planner for designing multi-probe insertions,utilizing the Allen Mouse Brain Common Coordinate Framework.
Proper citation: Pinpoint (RRID:SCR_023840) Copy
https://sites.google.com/view/brain-mapping
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.
Proper citation: brain-mapping (RRID:SCR_023845) Copy
http://bioconductor.org/packages/ABAEnrichment//
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.
Proper citation: ABAEnrichment (RRID:SCR_023814) Copy
https://github.com/alleninstitute/cocoframer
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.
Proper citation: Cocoframer (RRID:SCR_023817) Copy
http://hms-dbmi.github.io/brainmapr/
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.
Proper citation: Brainmapr (RRID:SCR_023816) Copy
https://www.nitrc.org/projects/cutnii/#
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.
Proper citation: CutNII (RRID:SCR_023824) Copy
https://github.com/macarenasa/goi2roimapping
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.
Proper citation: goi2roimapping (RRID:SCR_023820) Copy
https://miracl.readthedocs.io/en/latest/
Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.
Proper citation: MIRACL (RRID:SCR_020945) Copy
https://github.com/wildrootlab/SHARCQ
Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.
Proper citation: SHARCQ (RRID:SCR_022498) Copy
http://ibislab.ce.unipr.it/software/hippo/
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.
Proper citation: Hippo-ATESC (RRID:SCR_023809) Copy
https://github.com/xiaoqunwang-lab/Allendigger
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.
Proper citation: AllenDigger (RRID:SCR_023812) Copy
https://github.com/AllenInstitute/atlasplot
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.
Proper citation: Atlasplot (RRID:SCR_023810) Copy
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