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105 changes: 105 additions & 0 deletions Brain Image Library.md
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# Brain Image Library
## Description
The Brain Image Library (BIL) is a national public resource enabling
researchers to deposit, analyze, mine, share and interact with large brain
image datasets. BIL encompasses the deposition of datasets, the integration
of datasets into a searchable web-accessible system, the redistribution of
datasets, and a computational enclave to allow researchers to process
datasets in-place and share restricted and pre-release datasets. BIL is the
designated repository for microscopy data produced through the NIH BRAIN
Initiative.

# Roles
Please use [email protected] for any Brain Image Library issues or
questions in lieu of contacting people listed here directly.

[Primary Investigator] Alex Ropelewski ([email protected])
[MPI – Biologic Imaging] Simon Watkins ([email protected])
[MPI – Molecular Biosensors and Imaging] Marcel Bruchez ([email protected])
[Computational Hardware/Software] Greg Hood ([email protected])
[Networking Support] Kathy Benninger ([email protected])
[Image Data] Arthur Wetzel ([email protected])
[Website/Submission Portal] Luke Tuite ([email protected])
[Microscopy/Cell Biology] Alan Watson ([email protected])


## Objectives
* Permanent repository for high-quality brain microscopy datasets
– Brain images of mouse, rat, human, other mammals and model organisms
– Targeted experiments, including connectivity between cells and
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@carolth carolth Dec 6, 2019

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In some cases, like spatial transcriptomics data, repository may hold processed files instead of raw image files (although raw data is preferable). Should we clarify that in scope is hosting of derivative files from the image data? Morphology swc files is a similar example.

Oh, I see that is down below in the "in-scope"

spatial transcriptomics ( *FISH)
– Historical collections

* Provide HPC computing capability local to the data for pre-submission
data processing and post-submission exploration
– Enclave access to pre-release data
– Research access to restricted-access, secured data

* Provide user access and support


## In-scope
* Accept original microscopy image datasets from investigators. Provide text
for inclusion in Resource Sharing Plans. There is no-charge to contribute
data to BIL or access BIL services.
* Accept higher-level datasets of other types (e.g. neuron morphologies) that
are derived from or relate to image datasets housed at BIL.
* Provide data-transfer support including network analysis to find transfer
bottlenecks, a lendable portable disk (BrainBall) device and the ability to
receive extremely large datasets directly on LTO8 tape.
* Provide download access to all public datasets. Current supported
download methods include Globus and FTP.
* Provide project-only access to brain-initiative collaborations, allowing
collaborators to share and operate on datasets prior to publication.
* Provide stable DOIs that can be used in published literature to reference
specific datasets or images.
* Provide computational resources on which users can run applications that
operate directly on BIL-housed datasets.
* Host custom portals that can operate directly on BIL-housed datasets.
* Collaborate with investigators on establishing standardized formats,
pipelines, and services that can be adopted and/or made available through
BIL.


## Out-of-scope
* Performing analyses for users (e.g. registration or other analyses of
datasets)


# Communication
## Help Desk
For technical questions, assistance depositing files in BIL including
networking support, assistance retrieving data deposited in BIL or to comment
on our Web documentation.

Non-time critical issues:
Submit a help ticket. Send email to [email protected]

Time-critical issues:
Phone the PSC hotline at: 412.268.6350


## E-mail
Please use [email protected] for any Brain Image Library issues or
questions in lieu of contacting specific people listed.


## Website
Informational website containing instructions and current inventory:
http://www.brainimagelibrary.org/

Restricted-access authenticated submission portal for all submissions to BIL:
http://submit.brainimagelibrary.org/

The BIL is operated as a partnership between the Biomedical Applications
Group at the Pittsburgh Supercomputing Center, the Center for Biologic
Imaging (CBI) at the University of Pittsburgh, and the Molecular Biosensor and
Imaging Center at Carnegie Mellon University:
http://www.psc.edu/
http://www.cbi.pitt.edu/
http://pathways.mbic.cmu.edu/

## Funding
The Brain Image Library is supported by the National Institutes of Mental
Health of the National Institutes of Health under award number R24-MH-114793.
[NIH Reporter Link](https://projectreporter.nih.gov/project_info_description.cfm?aid=9737988&icde=47261137&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=)