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Platform Manuals

User Manual

A manual aimed at the end users of the platform, describing all our applications and APIs.

Also available in PDF format

Data Integration Manual

A document for data curators and integration specialists, describing in details our data integration processes.

Also available in PDF format

Technical Manual

A technical guide for developers with all the information about the Platform architecture and the data formats we are using.

Also available in PDF format

Acknowledgement

Finance information

This Platform was financed through the Human Brain Project, an European FET Flagship [ICT-2013.9.9], Grant agreement no: 604102.

The Neuroinformatics Platform would like to acknowledge the additional institutions and contributors:

  • INCF
    • Linda Lanyon
    • Mathew Abrams
  • Neuroscience Information Framework
    • Maryann Martone
    • Jeff Grethe
    • Tom Gillespie
    • Willy Wong

FAQ

What is NIP?

The Neuroinformatics Platform (NIP) will provide to the neuroscientist community with:

  • An integrated multi-level, data enriched atlas of the Human and rodent brain.
  • Analytics pipeline to automatically process sub-sets of data in order to provide an integrated view of the multi-level atlases to users.
  • 2D and 3D Viewers to navigate, query and annotate the atlases.
  • Programmatic API to access data in the atlases.

How do I sign-up?

All you need is to become a HBP Collaboratory member, a valid institution email address and to agree to our terms of use.

Visit the HBP webpage.

What are the Terms and conditions for use of NIP?

In order to access the NIP tools and Dataset, you have to agree on the following Terms of Use.

How can I become a contributor?

This documentation will guide you the Contributor Process.

What information should I provide when submitting a dataset?

For all submitted datasets into the Neuroinformatics should be accompanied with a standard set of metadata called MINDS (Minimum Information about a Neuroscience DataSet), please read this section to find out more.

What information should I provide when submitting a model?

In order to integrate the data, curate it and assess data quality the following information is required to be specified:

  1. What are the specific models (channels, cells, regions, etc) to be developed and their scientific objectives?
  2. What data are needed to constrain these models? What is the number of samples required and precision of the data necessary for the models?
  3. Is the data necessary coming from SP1-3 or outside of HBP? How many samples, what is the data format, what is the size of the data they are planning to deliver? How mature is the data production process?
  4. What features of the data are required to constrain the parameters and to validate the models?
  5. What quality level (e.g. signal-to-noise ratio, stain completeness, input resistance, etc) is required of the data to extract a sufficient number of the required features?
  6. Do feature extractors (analysis tools) exist or do they need to be developed? What are the data quality requirements of the feature extractors? Has this already been tested on actual datasets? What is the maturity of the feature extraction process?
  7. Do the data need to be combined or linked with other key data to be valuable? (For example do the electrophysiological recordings need to come from exactly the same cell as the morphological data?) Is this feasible?
  8. What are the curation requirements to make the data searchable and accessible by the model building and validation pipelines? For example, what are the properties that a query would need to be built on?
  9. What are the specific atlases required, who will be responsible for registering data to these atlases. Will the data be gathered with sufficient information/landmarks/etc to perform this registration?
  10. What are the computational and storage requirements for each dataset. Which size archival data repositories are required. Which size active data repositories are required and with which services. Do the services exist yet? What is the flow of data from depositing, staging, processing and deployment?
  11. Is the necessary metadata for data registration recorded with the data? These include: contributor, specimen details, methods/protocols, brain region/location, data type, data location). Is there sufficient location information or landmarks to register this data to a specific template brain atlas?

Under what licensing could I register my open access Dataset?

During the process of your open access dataset registration, a choice between 2 licenses will be required depending the commercial potential use of your Dataset. We strongly recommend you to carefully read the informations related to the following licenses in our ToS:

Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)

or

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

What file format can I upload?

The NIP platform will take any format submitted but we strongly recommend you inform yourself about which standard formats are recommended in the section about Specific Data Categories.

In any case, all published data should respects the ethical regulation described in our Terms of Use.

Who can access the file I upload ?

Depending of your restriction data policy you can select between:

  • Public access: metadata can be viewed and data downloaded by anybody
  • HBP Only access: metadata can be viewed by anybody but file download is restricted to HBP accredited users.

Can I modify / complete a previously download File?

Two possibilities:

  • The NIP provides a one-click registration process for open source data. Once published those data and the metadata associated are immutable.
  • Using the NIP restricted registration, you will be able to change the Metadata but not the uploaded immutable Dataset.

What is the maximum size of the data I can upload ?

Regarding Restricted access, you can upload unlimited files but 2GB per file is our size constraint. for large dataset, please contact directly the members of the NIP.

Who will use my data, for what purpose ?

Users will have to follow the NIP Terms of Use that contain the following piece of information: Use of the Data Set is restricted to academic, research, educational, government or other charitable or humanitarian purposes that are not-for-profit. The Data User is permitted to produce and distribute derived works from this Data Set provided that those derivatives are released under the same license terms as those accompanying this Data Set. Any other uses for the Data Set or its derived products will require explicit permission from the Contributor.

 When can I see my file ?

Everybody will be able to access your newly integrated information within a few days. After hitting the submit button, the NIP team will need a few days to register and curate your metadata. Your data will become “visible” in our Search client / Search API

How can I be sure the upload was complete?

Go to your « My Uploads » page (both in the NIP dataset registration page or on relative services webpages) and the status of your documents will be register.

General Information

Get Support

Report a general issue

Please do not hesitate to contact us, there are currently two ways to get in touch with the Neuroinformatics Team:

Report an Ethical Issue

If you believe an ethical outreach has happened, please fill in the following document.

Media Contact

For any press inquiries on the HBP:

EPFL ENT CBS BBP 2nd floor
Campus Biotech
Chemin des Mines 9
1202 Geneva
Tel: +41 (0)21 693 7660
Fax: +41 (0)21 693 7260

Traveling to Campus Biotech

By Train

From the Geneva airport, take the train to Geneva Cornavin (schedule here: Train connection, it takes 25 minutes trip between the airport and the Campus. From there, take bus 1 or 25 destination Jardin Botanique, stop “Mines” right in front of the main entrance, or the tram 15, stop “France” and then follow the directions to the Campus.

By Car

Follow the destination at this link. Once on site announce yourself as a BBP guest at the reception which will contact your host and let you into the building.

Disclaimer

Platform General Terms of use

Introduction

The Terms of Service (ToS) outline the HBP minimum standards for data sharing, access, authorship, citation, and restrictions of data and apply to all users of HBP Collaboratory data.

Users who register an account with the HBP agree to the Terms of Service. This includes agreement to comply with institutional rules and regulations.

If you do not accept the Terms and Conditions when applying for registration or thereafter, when using the Platform, you are not permitted to access or use the

Platform or post or submit any materials on it. HBP platforms and data are subject to European and national legislation and regulation and conform to the ethical principles of H2020. This means you may need the approval of your IRB or Ethics Committee to use the data. Different national, state and local laws may apply and be interpreted differently, so it is important that you consult with your IRB or Ethics Committee before beginning your research. If needed and upon request, the HBP collaboratory will provide a certificate stating that you have accepted the NIP Data use Terms and conditions.

Following EU principles, data funded by the EU should normally be available open access, unless there are valid reasons speaking against open access.

Data access requirements

Access to all HBP data and services is subject to requirements set forth by these Terms and Service to enable data providers to track usage, evaluate its impact in the Neuroscientists community, and confirm users’ acceptance of the terms of acceptable use. These requirements are standardized across the HBP to provide contractual exchange of data among the Contributors (defined below) within the HBP collaboratory and Data Users (defined below) that can be encoded into electronic form and exchanged between computers. This will allow direct access to data through a common portal once these requirements have been fulfilled.

The following registration information is required directly or by proxy prior to the transference of any Data Set:

  • Name
  • Affiliation
  • Institutional Email Address
  • Acceptance of the below General Data Use Agreement
  • A Statement of Intended Use that is compliant with the approved use defined below. Such statements may be submitted explicitly or made implicitly via the data access portal interface.

GENERAL TERMS OF SERVICE

IMPORTANT: PLEASE READ CAREFULLY. Use of the Data Set (defined below) is subject to the Terms of Service set forth below. By clicking this box, the Data User (defined below) agrees to be bound by these Terms and Conditions and enters into a legally binding Agreement with the Data Set Creator (“Agreement”). Users refusing to agree to the terms provided herein are not authorized to use the Data Set.

Definitions

Dataset. Digital data, either raw or derived, and its metadata provided through the data access portal interface, or through other media, including data and metadata derived from HBP monitoring protocols, field observations, collections, laboratory analysis, camera trap images, all written, recorded, graphic, audio, visual, and other materials in any media, whether or not subject to copyright protection, or the post-processing of existing data and identified by a unique identifier issued by the HBP.

All datasets provided by contributors (below v.) should have been produced following EC ethical regulation.

The HBP will not be held responsible for the data provenance.

Third Party Data Set. Digital data and its metadata provided through the data access portal interface, or through other media, not derived from HBP monitoring protocols, but provided by third party Data Set Creators.

Data Set Identifier. A unique identifier created by the information system to be included with a Data Set for the purpose of tracking and ongoing identification.

Data User. Individual to whom access to this Data Set may be granted, subject to acceptance of these Terms and Conditions by such individual and his or her immediate collaboration sphere, defined here as the institutions, partners, students and staff with whom such individual collaborates and to whom access must be granted in order to fulfill the such individual’s intended use of the Data Set.

Contributor. Individual or institution that produced the dataset. The data will be accessible to the whole community. Therefore, experimental data are not permitted. Moreover, no personal information related to patients or de-anonymized data are accepted.

Dataset Contact. Party designated in the accompanying metadata of the dataset as the primary contact for the dataset.

Data Registration. a unique set of information related to one specific dataset. It includes all piece of information required by the API or service registration pages as well as all piece of information about the Contributor registration, the contributors of the dataset and data user conditions.

Specific purpose

Use of the Data Set is restricted to academic, research, educational, government or other charitable or humanitarian purposes that are not-for-profit.

The Data User is permitted to produce and distribute derived works from this Data Set provided that those derivatives are released under the same license terms as those accompanying this Data Set.

Any other uses for the Data Set or its derived products will require explicit permission from the Contributor.

Limitation of use / approved use

The Data User agrees to the following terms:

  • The Data User may receive access to de-identified or aggregated data and in such cases will not attempt to establish the identity of, or attempt to contact any of the participants.
  • The Data User will not further disclose these data beyond the uses outlined in this agreement.
  • The Data User will require anyone on their team who utilizes these data, or anyone with whom they share these data to accept and comply with this data use agreement.
  • The Data User will comply with any rules and regulations imposed by their institutions and its institutional review board in requesting these data.
  • The Data User will ensure that Investigators who utilize HBP data use appropriate administrative, physical and technical safeguards to prevent use or disclosure of the data other than as provided for by this Agreement.
  • The Data User will report any use or disclosure of the data not provided for by this Agreement of which they become aware within 15 days of becoming aware of such use or disclosure. Reports/disclosures should be submitted to the HBP Point of Registration at www.hbp-pore.eu.

Users may not:

  • download, send or disseminate data containing viruses, worms, spyware, malware or any other similar malicious programs;
  • carry out any calculations, operations or transactions that may interrupt, destroy or restrict the functionality of the operation of EES or any program, computer or means of telecommunications; or
  • submit any information or materials that infringe third party rights, are libellous, obscene, threatening or otherwise unlawful.

Dual Use / Misuse

The HBP services and the associated data are provided for the purposes of peacetime Neuroscience and brain research. In particular all users of the HBP services and associated data must comply with the COUNCIL REGULATION (EC) No 428/2009, in particular Annex I LIST OF DUAL-USE ITEMS. Specifically all users of the HBP services and associated data confirm that any results derived from the use of these services are for the purposes of peacetime Neuroscience and brain research, are not for military use and are not in breach of said EC regulations.

Redistribution

The Data Set is provided for use by the Data User.

The metadata and these terms of service must accompany all copies made and be available to all users of this Data Set. The Data User will not redistribute the original Data Set for purposes other than those permitted (Approved use).

Attribution

The Data Set has been licensed in the spirit of open scientific collaboration.

The Data User agrees to offer clear and prominent attribution to the Contributor if such attribution is requested by the Contributor.

Citation

The Data User agrees to properly cite the Data Set, including the Data Set Identifier, in any publications or in the metadata of any derived data products that are produced using the Data Set.

Citation shall take the following general form:

  • Creator,
  • Year of Data Publication,
  • Title of Data Set,
  • Data Set Identifier
  • Where a data paper is available, then this should be cited,
  • Where a DOI is available, this DOI should be cited.

Acknowledgements

The Data User agrees to include the following acknowledgment in any publications where the Data Set contributed significantly to its content:

“Data in this publication were provided by the HBP. The HBP has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 650003.”

Individual data providers may have their own policies concerning the acknowledgements of their data.

In addition, the Data User agrees to include any additional acknowledgment of institutional support or specific funding awards provided in the metadata accompanying this Data Set, including those requested by the Contributor, in any publications where the Data Set contributes significantly to its content.

Licences

Data sets and third party data sets will be subject to licensing.

Users must adhere to these licences.

Details of licences can be provided by data owners.

Privacy

Collection of data from users is covered by the HBP privacy policy.

Termination

By accepting this Data Set, the Data User agrees to abide by the terms of this Agreement. The Contributor and its hosting institution are held responsible for any non compliance to the Data Set (above section a i.) provenance. Moreover, The Contributor and the HBP shall have the right to terminate this Agreement immediately by written notice upon the Data User’s breach of, or non-compliance with, any of its terms. The Data User may be held responsible for any misuse that is caused or encouraged by the Data User’s failure to abide by the terms of this Agreement. Consequences from failure to abide by these terms of service may include legal proceedings.

Disclaimer and Limits.

THE INFORMATION FROM OR THROUGH THE SITE IS PROVIDED “AS-IS,” “AS AVAILABLE,” AND ALL WARRANTIES, EXPRESS OR IMPLIED, ARE DISCLAIMED (INCLUDING BUT NOT LIMITED TO THE DISCLAIMER OF ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE). THE INFORMATION AND SERVICES MAY CONTAIN BUGS, ERRORS, PROBLEMS OR OTHER LIMITATIONS. HBP AFFILIATED PARTIES AND WE HAVE NO LIABILITY WHATSOEVER FOR YOUR USE OF ANY INFORMATION OR SERVICE. IN PARTICULAR, BUT NOT AS A LIMITATION THEREOF, HBP AND ITS AFFILIATED PARTIES ARE NOT LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES (INCLUDING DAMAGES FOR LOSS OF BUSINESS, LOSS OF PROFITS, LITIGATION, OR THE LIKE), WHETHER BASED ON BREACH OF CONTRACT, BREACH OF WARRANTY, TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY OR OTHERWISE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. THE NEGATION OF DAMAGES SET FORTH ABOVE ARE FUNDAMENTAL ELEMENTS OF THE BASIS OF THE BARGAIN BETWEEN THE DATA USER AND THE HBP. THIS SITE AND THE PRODUCTS, SERVICES, AND INFORMATION PRESENTED WOULD NOT BE PROVIDED WITHOUT SUCH LIMITATIONS. NO ADVICE OR INFORMATION, WHETHER ORAL OR WRITTEN, OBTAINED BY YOU FROM THE HBP THROUGH THE SITE SHALL CREATE ANY WARRANTY, REPRESENTATION OR GUARANTEE NOT EXPRESSLY STATED IN THIS AGREEMENT.

THE HBP DOES NOT PROVIDE LEGAL ADVICE NOR ENTER INTO ANY ATTORNEY-CLIENT RELATIONSHIP.

ALL RESPONSIBILITY OR LIABILITY FOR ANY DAMAGES CAUSED BY VIRUSES CONTAINED WITHIN THE ELECTRONIC FILE CONTAINING THE FORM OR DOCUMENT IS DISCLAIMED. THE HBP WILL NOT BE LIABLE TO YOU FOR ANY INCIDENTAL, SPECIAL OR CONSEQUENTIAL DAMAGES OF ANY KIND THAT MAY RESULT FROM USE OF OR INABILITY TO USE OUR SITE.

OUR MAXIMUM LIABILITY TO YOU UNDER ALL CIRCUMSTANCES WILL BE EQUAL TO THE PURCHASE PRICE THE DATA USER PAY FOR ANY GOODS, SERVICES OR INFORMATION.

Indemnification

The Data User agrees to indemnify, defend and hold the HBP and its partners, attorneys, staff, advertisers, product and service providers, and affiliates (collectively, “Affiliated Parties”) harmless from any liability, loss, claim and expense, including reasonable attorney’s fees, related to the data user’s violation of this Agreement or use of the Site.

Medical disclaimer

Materials on this Site have not been reviewed or approved by the European Medical Agency nor by the Food and Drug Administration.

All materials on this Site are provided for informational and review purposes. The HBP provides a resource that may be used for non-clinical research only. In no evident shall data be used in the provision of patient care. The HBP Medical Informatics Platform is not intended to and does not in any way substitute for professional medical advice.

The materials should not be relied upon for medical diagnosis or treatment, nor should you disregard the advice of your physical or other health care provider or delay seeking such advice due to anything you have read on or accessed through the Website. HBP assumes no responsibility for any injury and/or damage to person(s) or property as a matter of products and/or services liability, negligence or otherwise. Or from any use or operation of any methods, products, service, instruction or ideas contained in the material provided by the Site.

The content, organization, graphics, design, compilation, magnetic translation, digital conversion and other matters related to the Site are protected under applicable copyrights, trademarks and other proprietary (including but not limited to intellectual property) rights. The materials and services on this website are for personal non-commercial and non-clinical use. The copying, redistribution, use or publication by you of any such matters or any part of the Site is strictly prohibited.

Products and names mentioned on the Site may be trademarks of their respective owners. The HBP respects the intellectual property of others, and asks Data Users to do the same. If Data Users believe that their work has been copied in a way that constitutes copyright infringement, they should provide our Copyright Agent a self-certification stating that they are authorized to act on the copyright owner’s behalf, by directing an e-mail at: platform@humanbrainproject.eu

Arbitration

It is the policy of the HBP to make every reasonable effort to resolve all issues or disputes that may arise under this Agreement fairly by negotiation without litigation, if practicable. Any dispute arising out of or relating to this Agreement which is not settled by agreement of the parties shall be finally settled by arbitration in accordance with the UNCITRAL Arbitration Rules in force at the time the dispute arises.

Any disputes that cannot be resolved by negotiation shall be subject to arbitration using a single arbitrator. The arbitration shall take place in Geneva, in English, and the results of such arbitration shall be final, non-appealable, binding on each party, and enforceable in any court of competent jurisdiction. The terms and conditions of this Agreement shall be construed in accordance with the laws of Belgium, Brussels, without regard to any conflicts of laws principles.

Severability

In the event that any one or more of the provisions contained herein shall, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, but this Agreement shall be construed as if such invalid, illegal or unenforceable provisions had never been contained herein, unless the deletion of such provision or provisions would result in such a material change so as to cause completion of the transactions contemplated herein to be unreasonable.

Waiver

HBP may specifically and expressly waive any breach of this Agreement by Data User, but no such waiver shall constitute a continuing waiver of similar or other breaches. HBP’s consent or approval of any act by Data User shall not be deemed to render unnecessary the consent to or approval of any subsequent act by Data User.

Entire agreement

This Agreement constitutes the entire understanding between the parties with respect to its subject matter hereunder, is intended as a complete and exclusive statement of the terms of their agreement, and supersedes any prior or contemporaneous agreements or understandings relating to the subject matter hereunder.

Acknowledgement /acceptance of agreement

The Data User agrees to the terms and conditions outlined in this Terms of Use Agreement (“Agreement”) with respect to the HBP’s site (the “Site”). This Agreement constitutes the entire and only agreement between us and you, and supersedes all prior or contemporaneous agreements, representations, warranties and understandings with respect to the Site, the content, products or services provided by or through the Site, and the subject matter of this Agreement.

The HBP may amend this Agreement at any time without specific notice to the Data User.

The latest Agreement will be posted on the Site, and the Data User should review this Agreement prior to using the Site.

Changes to the Terms of Service

The HBP Platforms may, at any time, vary, add to or delete any provision of these Terms and Conditions.

Users and their organisations expressly acknowledge and agree that such new terms and conditions.

Any access to or use of the HBP shall constitute unconditional acceptance of these Terms of Service (in the then-current version).

HBP Data Registration Declaration

A specific section of or Term of Service regarding HBP Data Registration can be found here. Please, read carefully this documentation if you consider becoming a contributor.

HBP Data Registration Declaration

HBP Data Registration Declaration

This is the structure of a data registration declaration that details the various aspects that a data owner would need to agree to, in order to ensure ethical compliance of the data. This declaration clarifies questions concerning the registration of data, focusing on ethics and compliance issues. For further information, and complementary agreement, please read our Disclaimers.

Authorisation

  • I have accepted the HBP’s Terms of Service.
  • I am authorised to register the data and give permission for the subsequent uses of the data for the purposes of the HBP.
  • I give permission for the use of this data:
    • For internal use of the HBP only. Internal use will be covered by the Grant Agreement and the Consortium Agreement.
    • For use covered by a specific data use agreement, if so state which one.
    • For any use covered by the terms of service of the HBP.

Compliance

I confirm that the data registered with the HBP was collected in research that complied with:

  • applicable international, EU and national law
  • ethical principles as indicated by the Horizon 2020 Ethics Self Assessment
  • IRB approval where applicable
  • the Horizon 2020 Data Management Guidelines see PDF

Audit

I confirm that I have access to documents that demonstrate the ethics compliance of the data. I am willing to comply with an audit by an appropriate body and am willing to provide the above evidence to the HBP within 30 calendar days of receiving a request.

Sanctions

I am aware that failure to provide relevant evidence to an HBP audit can lead to the removal of the data from the HBP systems, the closing of my user account and/or a notification to my institution’s ethics bodies concerning potentially unethical practice.

Data use

I give permission for the use of this data:

  1. For internal use of the HBP only. Internal use will be covered by the Grant Agreement and the Consortium Agreement
  2. For use covered by a specific data use agreement, if so state which one
  3. For any use covered by the terms of service of the HBP.

License

During the process of your « open access Data registration » a choice between 2 licenses will be required depending the commercial potential use of your Dataset. We strongly recommend you to carefully read the informations related to the following licenses in our ToS: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) or Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

Data sets and third party data sets will be subject to licensing. Users must adhere to these licences. Details of licences can be provided by data owners.

Acknowledgement

The Data User agrees to the terms and conditions outlined in this Terms of Use Agreement (“Agreement”) with respect to the HBP’s site (the “Site”).

This Agreement constitutes the entire and only agreement between us and you, and supersedes all prior or contemporaneous agreements, representations, warranties and understandings with respect to the Site, the content, products or services provided by or through the Site, and the subject matter of this Agreement. The HBP may amend this Agreement at any time without specific notice to the Data User.

The latest Agreement will be posted on the Site, and the Data User should review this Agreement prior to using the Site.

GENERAL TERMS OF SERVICE

IMPORTANT: PLEASE READ CAREFULLY. Use of the Data Set (defined below) is subject to the Terms of Service set forth below. By clicking this box, the Data User (defined below) agrees to be bound by these Terms and Conditions and enters into a legally binding Agreement with the Data Set Creator (‘Agreement’). Users refusing to agree to the terms provided herein are not authorized to use the Data Set.

Changes to the Terms of Service

The HBP Platforms may, at any time, vary, add to or delete any provision of these Terms and Conditions.

Users and their organisations expressly acknowledge and agree that such new terms and conditions.

Any access to or use of the HBP shall constitute unconditional acceptance of these Terms of Service (in the then-current version).

The content, organization, graphics, design, compilation, magnetic translation, digital conversion and other matters related to the Site are protected under applicable copyrights, trademarks and other proprietary (including but not limited to intellectual property) rights. The materials and services on this website are for personal non-commercial and non-clinical use. The copying, redistribution, use or publication by you of any such matters or any part of the Site is strictly prohibited.

Products and names mentioned on the Site may be trademarks of their respective owners. The HBP respects the intellectual property of others, and asks Data Users to do the same. If Data Users believe that their work has been copied in a way that constitutes copyright infringement, they should provide our Copyright Agent a self-certification stating that they are authorized to act on the copyright owner’s behalf, by directing an e-mail at: platform@humanbrainproject.eu

Medical disclaimer

Materials on this Site have not been reviewed or approved by the European Medical Agency nor by the Food and Drug Administration.

All materials on this Site are provided for informational and review purposes. The HBP provides a resource that may be used for non-clinical research only. In no evident shall data be used in the provision of patient care. The HBP Medical Informatics Platform is not intended to and does not in any way substitute for professional medical advice.

The materials should not be relied upon for medical diagnosis or treatment, nor should you disregard the advice of your physical or other health care provider or delay seeking such advice due to anything you have read on or accessed through the Website. HBP assumes no responsibility for any injury and/or damage to person(s) or property as a matter of products and/or services liability, negligence or otherwise. Or from any use or operation of any methods, products, service, instruction or ideas contained in the material provided by the Site.

HBP Collaboratory Tools

How to access the NeuroInformatics Platform tools?

We provide you with Structural data analysis, functional analysis as well as brain atlases tools that have been specifically developed in order to help neuroscientists to retrieve information and visualize dataset can be easily find within our NeuroInformatics Platform.

The different tools are listed within our Neuroinformatics Platform Collaboratory section.

Here is a non exhaustive list of HBP collaboratory NIP tools available:

  • Structural Data Analysis Tools:
    • EspINA
      EspINA is a user-friendly tool which performs segmentation and analysis of elements in a reconstructed 3D volume of the cerebral cortex, and greatly facilitates and accelerates these processes. It allows visualization and segmentation of large image stacks datasets, both from electron microscopy (e.g. FIB/SEM) and light microscopy.
      Link: website, user manual
    • 3DSomaMS
      3DSomaMS is an R package for soma reparation, segmentation and characterization.
      Link: website, user manual
  • Functional Analysis Tools:
  • Brain Atlases Tools:
    • AligNII
      Web-based tool for anchoring 2D image data into 3D atlas space
      Link: website, user manual
    • Scalable Brain Atlas
      The Scalable Brain Atlas (SBA) is a fully web-based display engine for brain atlases, imaging data and topologies. It allows client websites to show brain region related data in a 3D interactive context and provides services to look up regions, generate thumbnails or download nomenclature and delineation data.
      Link: website, user manual
    • QuickNII
      Standalone tool for anchoring 2D image data into 3D atlas space.
      Link: website, user manual
    • Morphology Viewer
      Web-based 3D neuron morphology viewer.
      Link: website, user manual
    • Synapse Generator
      SynapseGenerator is a pipeline used to predict connectivity at the synapse level.
      Link: website, user manual
    • MeshView
      Web-based mesh viewer with user-defined cut plane support
      Link: website, user manual
    • MeshGen
      Mesh generator for volumetric segmentation data.
      Link: website, user manual
    • CutNII
      Standalone viewer for volumetric atlases with custom-angle slicing support
      Link: website, user manual