DataJoint Neuro has completed a one-year project with the Svoboda Lab at the Janelia Research Campus. The project features DataJoint pipelines with export capability to the Neurodata Without Borders (NWB 2.0) format of electrophysiology and behavioral data from 11 published papers. The project is publicly available at https://github.com/vathes/DataJoint-NWB-showcase. Visit our poster at SfN2019 (DD27 - Oct 21st 1-5PM) to learn more!
DataJoint Neuro's scientists Shan Shen and Jacob Reimer presented DataJoint for imaging pipelines in a talk and software demo at the Bioimage Informatics conference at the Allen Institute for Brain Science in Seattle, WA.
DataJoint Neuro’s scientists Thinh Nguyen and Edgar Y. Walker visited the Moser Lab at Trondheim, Norway to hold a DataJoint workshop. The workshop featured a DataJoint pipeline for electrophysiology and behavioral tracking, built in collaboration with the Moser team, and showcased the workflow surrounding this pipeline.
Dimitri Yatsenko presented "Data Pipelines for Neuroscience" in the Neuroinformatics Workflows Session of the Neuroinformatics 2019 Conference in Warsaw organized by the International Neuroinformatics Coordinating Facility.
See the presentation here.
DataJoint Neuro's data scientist Shan Shen conducted a workshop at the IBL Code Camp hosted at Columbia University from 9/2/2019 to 9/6/2019. Shan gave an introduction to the IBL DataJoint pipeline to the IBL contributors and participated in the IBL Hackathon to help develop a data pipeline for model fitting.
DataJoint Neuro has renewed the agreement to support the development of experiment data pipelines for the Mesoscale Activity Project. The open-source code for this pipeline, including electrophysiology, behavior, histology, and video tracking data is available on GitHub: https://github.com/mesoscale-activity-map/map-ephys.
Currently, the team is implementing an automatic report generation process and adding mechanisms to improve cross-lab data sharing for machine learning and modeling efforts. Later in the year, efforts will expand into adding web-based visualization and navigation to allow more casual access to the data to the wider Neuroscience community.
DataJoint Neuro has renewed the agreement to support and co-develop the computational data pipelines for the International Brain Lab project. We are looking forward to another fruitful year!
DataJoint Neuro's data scientist Shan Shen conducted a workshop to introduce the Mesoscale Activity Project data pipeline to Shaul Druckmann’s lab at Stanford University on 6/28/2019. Chris and Thinh have been helping develop the pipeline over the past two years and now the data pipeline is ready for the theoretician to work with.
DataJoint Neuro has renewed the agreement to support and co-develop the data pipelines for the Princeton U19 project. We are excited to help the team use DataJoint to build more powerful data pipelines!
DataJoint Neuro's data scientist Shan Shen conducted a workshop at Princeton University from 5/13/2019 to 5/15/2019. Shan gave an overview of the current status of the data management system within the U19 team and performed a tutorial on the current U19 DataJoint behavioral pipeline. The next phase will focus on the imaging pipeline.
DataJoint Neuro’s scientists Thinh Nguyen and Edgar Y. Walker visited the Moser Lab at Trondheim, Norway, embarking on a new project of designing comprehensive DataJoint pipeline for electrophysiology and behavioral tracking of freely moving animals. The pipeline is designed to handle and unify multiple types of recording systems and tracking systems. The pipeline will also capture a scientific workflow, from data recording, spike clustering using various techniques to data analyses and reporting. We are extremely honored and excited to start on this challenging project!
Vathes welcomes Raphael Guzman, a University of Houston Alumnus, who joins the company in the role of Software Engineer. As a technical professional with 10 years in software and network engineering, Raphael brings proficiency in Web Services, IoT, Edge appliance development, Computational Fluid Dynamics, and Finite Element Modeling. Among other projects, Raphael will join forces with the DataJoint library development team, in particular driving the MATLAB development forward.
Vathes is thrilled to extend the ongoing project with Moser group from Kavli institute to now support the development and extension of multi-photon imaging data pipelines, in addition to the continued involvement and development of the electrophysiology pipeline in freely behaving animals. The pipeline aims to seamlessly connect data acquisition, pre-processing, and behavioral analysis.
Vathes successfully completed the pilot phase of an ongoing project with UCSD. The project aims to establish an overarching data pipeline and workflow using DataJoint for a multi-lab collaborative large scale microscopy neuroimaging project, aiming to define/expand mouse brain atlases using machine learning approaches. As a core component of the project, Neuroglancer will be used as the web-based, 3D visualization and annotation software. To this end, Vathes is committed to develop and support toolsets for seamless integration between DataJoint and Neuroglancer.
Vathes has successfully completed Milestone 2 of our contract with the International Brain Laboratory (IBL), where we developed data pipelines to handle the core mouse and behavioral information collected through IBL projects. In Milestone 3, Vathes will continue to develop and extend the data pipeline, and we are excited to be developing a web interface to support intuitive navigation of the massive behavioral and electrophysiological data collected by IBL.
The 2019 Neuro Reproducibility Hackashop saw the presentation of many exciting developments for researchers and tool builders within the Neuroscience community. With the goal of promoting reproducibility and interoperability of neuro toolsets, Vathes has worked closely with community leaders and tool builders and is committed to multiple upcoming interoperability efforts. Specifically, Vathes engineers have worked closely with NWB developers to outline a practical and effective pathway for enabling export capabilities from DataJoint pipelines into NWB 2.0 files. Furthermore, we are very excited to start an interoperability project with the Gigantum team, in which a DataJoint pipeline can be configured to be used as an input to a Gigantum project.
Vathes conducted a 3 day DataJoint workshop at Princeton as part of our continued involvement with Princeton U19 project. We were excited to cover topics ranging from DataJoint introduction, infrastructure setup and management as well as hands-on design and implementation of data pipelines. Vathes will continue to be involved in Princeton’s U19 project, providing support on data pipeline development and deployment.
Vathes LLC has launched a project in collaboration with Karel Svoboda's Lab at the Janelia Research Campus of the Howard Hughes Medical Institute to showcase DataJoint pipelines for their recent publications. Each pipeline will have the ability to export data into the Neuroscience Without Borders 2.0 format. The project will be completed in the fall of 2019 and its home page will be https://github.com/vathes/NWB-showcase
Vathes is excited to have Thinh Nguyen join the team. Thinh has a Ph.D. in Biomedical Engineering from University of Houston, specialized in computational neuroscience, where he developed methodology for multimodal integration of EEG and fMRI toward neuroimaging research. Thinh is also highly passionate in the field of Machine Learning and A.I. in neuroscience applications. As a Data Scientist at Vathes, Thinh is very excited to use his computational neuroscience and programming background toward building data engineering solutions for scientists to advance the field of Neuroscience.
In October Vathes began a contract with Matt McGinley to support him as he transitions his behavioral and neural data acquisition to DataJoint pipelines.
From September 26-28, 2018, the Vathes team will be attending the Bernstein Conference as an exhibitor. The Bernstein Conference is the largest annual Computational Neuroscience conference in Europe, and Vathes is looking forward to sharing information about our services with attendees.
Vathes is excited to welcome Austin Hilberg and Shan Shen to the team. Austin Hilberg has a Ph.D. in Biomedical Engineering from UCLA, where he studied the human visual system and visual attention control using fMRI and EEG. Since graduating, he has been working in Silicon Valley developing medical ultrasound systems. In his spare time, he enjoys creating virtual reality experiences and tinkering with electronic devices. Austin is very excited to apply his engineering, programming, and neuroscience background to his role as a Data Scientist at Vathes. Shan Shen has a Ph.D. in Neuroscience from Baylor College of Medicine. During her graduate training, she studied feedback circuits in mouse visual cortex with a wide range of techniques including optogenetics, imaging and electrophysiology. She also has experience working on human visual psychophysics, using Bayesian modeling. Throughout her academic career, she has been using DataJoint to organize data and facilitate analysis. With a combination of experience in experiments, modeling, and data analysis, Shan is very excited to work as a Data Scientist at Vathes and is looking forward to helping neuroscientists build efficient pipelines for data analysis.
Vathes entered into a contract with Princeton Neuroscience Institute (PNI) to complete thorough technical reference documentation for DataJoint by December 15, 2018.
Building off a January Workshop for the Princeton U19 group, Vathes and the Princeton Neuroscience Institute (PNI) officially entered a contract. Vathes will provide support for developing DataJoint pipeline for their U19 projects and support the adoption of DataJoint by PNI labs.
DataJoint was elected as the official platform for the data collection and analysis for the International Brain Lab (IBL). Over a one-year period, Vathes will work with participating labs to develop a data pipeline and support related developments in the DataJoint framework and web visualization platforms.
Working closely with Moser group and BIOINFORX developers, Vathes completed the design of a DataJoint data pipeline to represent data stored in mLIMS and developed a utility to continuously synchronize data entered into mLIMS((https://bioinforx.com/lims2/product_mlims.php) into the DataJoint pipeline.
Edgar Y. Walker and Dimitri Yatsenko ran a two-day workshop on DataJoint sponsored by NeuroNex. The workshop was open to the public and targeted researchers with an interest in stronger data organization tools who had no prior experience working with DataJoint. Edgar led the workshop as the primary instructor.
Day one covered introductory topics with demonstrations and exercises throughout the workshop. Day two covered hands-on applications of DataJoint, such as building a data pipeline from scratch for an existing project and extending an existing data pipeline with new analysis tables. Edgar also reviewed best practices for integrating DataJoint with other technologies such as GitHub and Docker.
All workshop materials are available at https://github.com/datajoint/neuronex_workshop_2018, and the videos are available at the following link.
Introduction - Dimitri Yatsenko presents the background, motivation, and overview of DataJoint.
Sessions 0-7 • Session 0 – Getting Connected - Edgar Y. Walker describes how to set up DataJoint to connect with a database server.
• Session 1 – Getting Started with DataJoint - Edgar Y. Walker presents background concepts of a data pipeline, and shows how to use DataJoint to define a first pipeline with manual tables. He then shows how to insert, query, and delete data in the pipeline.
• Session 2 – Imported and Computed Tables - Edgar Y. Walker shows how to extend a data pipeline with imported tables to import and store data present in external files. He then demonstrates how to define computations and their results as computed tables in the pipeline, taking a simple spike detection algorithm as an example.
• Session 3 - Design Patterns and Complex Query - Edgar Y. Walker revisits design patterns encountered in the example pipelines and discusses pipeline design. He then covers multiple advanced query exercises.
• Session 4 – Case Study 1 - Edgar Y. Walker presents a case study for designing a new data pipeline based on a specific research project.
• Session 5 – Case Study 2 - Edgar Y. Walker presents a case study where the students extend an existing data pipeline with new computations.
• Session 6 - Best Practices for Pipeline Design and Maintenance - Edgar Y. Walker presents various tools and technologies that can be used together with DataJoint to facilitate data sharing and reproducible research. In particular, Edgar covers Git, GitHub and Docker.
• Session 7 - Future Developments, Resources and Workshop Recap - Dimitri Yatsenko discusses the upcoming roadmap for DataJoint and surrounding technology development. Edgar Y. Walker then provides a recap of the workshop and discusses further learning resources.
Dimitri Yatsenko and Edgar Y. Walker visited the Moser group (2014 Nobel Laureates) at NTNU Kavli Institute to present on DataJoint. During the visit, Vathes reached an agreement to develop a DataJoint data pipeline that will stay synchronized to mouse and rat colony data organized and managed by mLIMS. This development will allow the Moser group to have unified access to information relevant for experimental data collection and analysis through DataJoint, while at the same time leveraging well-established solutions for specialized data entry and management, such as the animal colony information handled by mLIMS.
Dimitri Yatsenko and Edgar Y. Walker travelled to the UK to present DataJoint to Kenneth Harris's group at UCL and discussed the integration of DataJoint with International Brain Lab projects.
Dimitri Yatsenko and Edgar Y. Walker travelled to Princeton Neuroscience Institute (PNI) to run a two-day introductory workshop on how to build neuroscience data pipelines using DataJoint. Approximately fifty researchers involved with the Princeton U19 program attended the workshop. On the first day, Dimitri and Edgar covered the basic principles and concepts of DataJoint. On day two, they covered applied examples, and the participants translated an existing project into the DataJoint pipeline with support from the instructors.
Vathes sponsored an exhibit at the 2017 Society for Neuroscience conference. We were thrilled to meet with lots of neuroscientists interested in learning about DataJoint and we were delighted to meet existing users!
Vathes presented the DataJoint framework at the Systems Neuroscience Club at Harvard Medical School, which was followed by discussions with several neuroscience labs who are using or considering to adopt DataJoint for their data pipelines.
Vathes welcomes Christopher Turner, who joined the company in the role of a product engineer in July. A technical professional with 15 years of software and systems development, Chris will lead efforts in software development and operations support.
Vathes LLC began work under a service agreement to build and support the data pipeline for the multi-lab collaborative project nicknamed the “Mesoscale Activity Project” or MAP. This three-year project aims to analyze brain-wide neural activity during behavior and publish the datasets for the general scientific community. A more detailed description of the project can found at
Dimitri and Edgar presented at the University of Utah and spent a full day learning about the cutting-edge neuroscience research conducted at the University of Utah, and discussing how DataJoint might be able to help!
Dimitri and Edgar presented at Janelia Farm and spent two days meeting with a number of interested labs there.
Checkout the recording of their full presentation!