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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/jtsiomb/meshgen

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.

Proper citation: MeshGen (RRID:SCR_023819) Copy   

•   Source: SciCrunch Registry

https://abagen.readthedocs.io/en/stable/

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.

Proper citation: Abagen (RRID:SCR_023832) Copy   

•   Source: SciCrunch Registry

https://github.com/chrisgorgo/alleninf

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.

Proper citation: Alleninf (RRID:SCR_023837) Copy   

•   Source: SciCrunch Registry

https://github.com/cortex-lab/allenCCF

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

Proper citation: allenCCF (RRID:SCR_023830) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/morphapi

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.

Proper citation: MorphAPI (RRID:SCR_023851) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-splitter

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

Proper citation: Atlas Splitter (RRID:SCR_023842) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-direction-vectors

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

Proper citation: Atlas Direction Vectors (RRID:SCR_023841) Copy   

•   Source: SciCrunch Registry

https://github.com/itsasimiqbal/SeBRe

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

Proper citation: Segmenting Brain Regions (RRID:SCR_023849) Copy   

•   Source: SciCrunch Registry

https://quadbio.github.io/VoxHunt/

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.

Proper citation: VoxHunt (RRID:SCR_023829) Copy   

•   Source: SciCrunch Registry

http://www.linked-neuron-data.org/

Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.

Proper citation: Linked Neuron Data (RRID:SCR_003658) Copy   

•   Source: SciCrunch Registry

https://github.com/Nexusger/AllenMouseBrainImageLoader

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).

Proper citation: Allen Mouse Brain ImageLoader (RRID:SCR_023827) Copy   

•   Source: SciCrunch Registry

https://bbp.epfl.ch/nexus/cell-atlas/

Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access.

Proper citation: Blue Brain Cell Atlas (RRID:SCR_019266) Copy   

•   Source: SciCrunch Registry

http://kimlab.io/brain-map/atlas/

Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.

Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/explore/seattle-alzheimers-disease

Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute.

Proper citation: Seattle Alzheimer Disease Brain Cell Atlas (RRID:SCR_023110) Copy   

•   Source: SciCrunch Registry

http://brainstars.org

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.

Proper citation: BrainStars (RRID:SCR_005810) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

https://github.com/ejcorn/mouse_abi_tool

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

Proper citation: Mouse_abi_tool (RRID:SCR_023831) Copy   

•   Source: SciCrunch Registry