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Sustainability Roadmap between DataJoint Elements and Suite2p

datajoint suite2p

Aim

DataJoint Elements and Suite2p are two neuroinformatics initiatives in active development. The projects develop independently yet they have complementary aims and overlapping user communities. This document establishes key processes for coordinating development and communications in order to promote integration and interoperability across the two ecosystems.

Projects and Teams

DataJoint

DataJoint Elements — https://datajoint.com/docs/elements/ — is a collection of open-source reference database schemas and analysis workflows for neurophysiology experiments, supported by DataJoint — https://datajoint.com/docs/core/ — an open-source software framework. The project is funded by the NIH grant U24 NS116470 and led by Dr. Dimitri Yatsenko.

The principal developer of DataJoint Elements and the DataJoint framework is the company DataJoint — https://datajoint.com.

Suite2p

Suite2p — https://www.suite2p.org — is a pipeline for processing calcium imaging data. The project is funded by HHMI Janelia Research Campus and led by Dr. Carsen Stringer and Dr. Marius Pachitariu.

The principal developers of Suite2p are at the Janelia Research Campus.

General Principles

No obligation

The developers of the two ecosystems acknowledge that this roadmap document creates no contractual relationship between them but they agree to work together in the spirit of partnership to ensure that there is a united, visible, and responsive leadership and to demonstrate administrative and managerial commitment to coordinate development and communications.

Coordinated Development

The two projects will coordinate their development approaches to ensure maximum interoperability. This includes:

  • coordinated use of terminology and nomenclatures
  • support for testing infrastructure: unit testing and integration testing
  • a coordinated software release process and versioning
  • coordinated resolution of issues arising from joint use of the two tools

Points of Contact

To achieve the aims of coordinated development, both projects appoint a primary point of contact (POC) to respond to questions relating to the integration and interoperability of DataJoint Elements and Suite2p.

For 2022, the DataJoint Elements POC is Dr. Kushal Bakshi (kushal@datajoint.com)

For 2022, the Suite2p POC is Dr. Carsen Stringer (stringerc@janelia.hhmi.org)

Annual Review

To achieve the aims of coordinated development, the principal developers conduct a joint annual review of this roadmap document to ensure that the two programs are well integrated and not redundant. The contents and resolutions of the review will be made publicly available.

Licensing

The two parties ensure that relevant software components are developed under licenses that avoid any hindrance to integration and interoperability between DataJoint Elements and Suite2p.

Development Roadmap

  • Tests to verify loading Suite2p data - Pytests
  • Tests to verify running Suite2p - Pytests

Citation

If you use Suite2p please cite Pachitariu et al., bioRxiv 2017 in your publications.