DataJoint History

Academic Origins: From Lab Tool to Open-Source Project¶

The story of DataJoint begins in 2008 in Dr. Andreas Tolias’s neuroscience lab at Baylor College of Medicine. The lab was tackling complex neurophysiology experiments, and a group including Alex Ecker, Philipp Berens, Andreas Hoenselaar, and R. James Cotton had already created a MATLAB library called “Steinbruch” that used MySQL to manage data.

Building on these ideas, I began to formalize a new approach in the fall of 2009. My goal was to design a system based on rigorous relational principles that could naturally represent a scientific workflow, with native support for computational dependencies—a feature missing from mainstream database models. This led to the first version of DataJoint for MATLAB, which I developed and applied to my own neurophysiology experiments.

By 2011, with the help of early adopters Manolis Froudarakis and Jacob Reimer, DataJoint was fully integrated into our lab’s workflow. Recognizing its potential, Dr. Tolias supported its broader release, and I launched DataJoint as an open-source project on Google Code. By the time I defended my Ph.D. in 2014, the framework was already in use at research institutions worldwide.

Although I had started a Python version in 2011, it gained serious momentum between 2014 and 2015 when lab members Edgar Y. Walker and Fabian Sinz joined the effort to create a full Python package. The Tolias lab’s participation in the IARPA MICrONS project ^[1] further validated DataJoint’s approach. Its ability to manage the work of a large, multidisciplinary team proved essential and significantly boosted its adoption in the scientific community.

Commercialization: From Consulting to a Collaborative Platform¶

As DataJoint’s user base grew, so did the need for professional support. In 2016, Dimitri Yatsenko, Jacob Reimer, Edgar Y. Walker, and Andreas Tolias founded Vathes LLC to provide data engineering and consulting services to research labs, spurred by a DARPA initiative to commercialize neuroscience tools.

In 2017, Vathes received a Phase I SBIR grant, allowing Edgar and me to balance company operations with our academic work. The team expanded in 2018 with key members Shan Shen, Thinh Nguyen, Chris Turner, and Raphael Guzman, who were crucial in developing the framework and integrating it into large-scale lab workflows. Collaborations with Prof. Carlos Brody and Prof. Karel Svoboda also significantly increased its use.

The year 2020 was pivotal. A major 5-year NIH grant enabled the development of DataJoint Elements—a collection of curated data pipelines for neuroscience. This initiative was advanced by Dr. Kabilar Gunalan, who joined the team and played a vital leadership role. In 2021, we rebranded the company as DataJoint to reflect our core product and shifted our focus to commercial technology for research collaboration, at which point I transitioned to a full-time role as CEO.

In 2022, a Phase II SBIR commercialization grant from the NIH funded the development of our online collaborative platform: the DataJoint Platform. Monty Kosma, who joined that year, spearheaded the platform’s development, eventually becoming a co-founder and President and guiding the company’s transformation into a product-focused enterprise.

The DataJoint Platform officially launched in 2024, empowering its first cohort of labs. In the fall of that year, the company entered a new phase of growth with the addition of Jim Olson, former CEO of the data operations platform Flywheel.io. Jim’s appointment as CEO in December 2024 brought fresh strategic vision to scale the company’s impact.

In August 2025, DataJoint Inc. raised its seed round, bringing in venture capital and bolstering its vision to accelerate the platform’s development.

Today, DataJoint embodies a unique blend of community-driven open-source development and a powerful online platform. This dual approach ensures our tools remain accessible and continuously evolving while providing researchers with a secure, collaborative environment to advance their work.