Educational Tutorials
Educational Tutorials
These tools are organized by a description of their functionality, their RRID (Research Resource Identification), the type of resource, data modality, and which Allen Institute resource's data was utilized for this tool. The authors of the tool are listed first by computational contributors then by academic authors when the tool has a relevant publication.
A Course-based Research Experience Using Allen Brain Map
This resource mimics a course for users to utilize Allen Brain Map resources and develop a research question, document their methodology and results, and eventually present their work in a conference environment.
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Type of Resource |
educational tutorial |
|
Modality |
general Allen Brain Map data |
|
Author |
Jim Ryan, Kaitlyn Casimo |
|
Year Released |
2021 |
AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures
The Atlas Ontology Model (AOM) identifies and defines the relationships between four common atlases and characterizes their properties and organization. This model can serve as a suggestion for minimum requirements for atlases to accelerate neuroscience data integration.
|
RRID |
|
|
Type of Resource |
educational, data integration tool |
|
Modality |
ontology |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Common Coordinate Framework |
|
Author |
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Time Dickscheid, Jan G. Bjaalie, et al. |
|
Year Released |
2011 |
Learning How to Code While Analyzing an Open Access Electrophysiology Dataset
This resource is a lesson plan for users to begin coding in Python and interact with and analyze electrophysiology data from the Allen Institute for Brain Science.
|
Type of Resource |
educational tutorial |
|
Modality |
electrophysiology |
|
Allen Resource Utilized |
Allen Cell Types Database |
|
Author |
Ashley Juavinett |
|
Year Released |
2020 |
QUINT
The QUINT workflow includes a suite of various software to form an analysis pipeline of atlas-based quantification of labeled features in histological images from a mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together.
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RRID |
|
|
Type of Resource |
workflow tutorial, educational |
|
Modality |
histology, imaging |
|
Allen Resource Utilized |
Allen Common Coordinate Framework |
|
Author |
Sharon Yates, Nicolaas Groeneboom, Christopher Coello, Stefan Lichtenthaler, Peer-Hendrik Kuhn |
|
Year Released |
2019 |
Disclaimer
This list of third-party tools utilizing Allen Brain Map resources is for informational purposes only and do not constitute an endorsement or approval by Allen Institute of any of the tools or other products, services, or opinions of the associated organizations. Allen Institute bears no responsibility for the accuracy, legality, or content of the external tools or for that of subsequent links. The descriptions of these tools were adapted from their individual websites.
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