DataJoint is a Houston-based company whose mission is to build and operate a science orchestration platform that eliminates barriers for researchers who rely on automation, AI, and high-performance computing. Our projects include:
DataJoint Core: open-source Python and MATLAB APIs for defining and operating computational data pipelines—sequences of steps for data acquisition, processing, and transformation—via a MySQL backend.
DataJoint Elements: a growing compilation of community-curated, open-source software modules for building automated data pipelines and analysis workflows for neuroscience experiments.
DataJoint Works: a cloud-based platform that hosts pipelines built via Core and Elements, facilitating collaboration and reanalysis.
The Allen Institute’s Brain Observatory is a huge repository of publicly available two-photon Calcium imaging data. DataJoint’s Element Calcium Imaging offers automation in standard preprocessing methods, including Suite2p and CaImAn. This project aims to :
Develop mechanism to ingest Brain Observatory data into the Element.
Demonstrate reanalysis of this data via jupyter notebook
Add unit tests for the above mechanism.
Automate this process on the Works platform to permit replication by any Works user.
Skill level: Novice/advanced
Required skills: Python, calcium imaging data analysis
Hello @dimitri@kabilar Sir!
I’m Viren Varma, I’m a senior at NIT Karnataka, I’m applying for gsoc’23. I’m relatively new to open source. But I have a vast knowledge of deep learning, computer vision and Bio-informatics through personal and course projects. I’ve got experience in working in python and data science. Both the projects from Datajoint really align with my interests and I’d love to work on it. Can you guide me on getting started with the project? Or if there’s a separate slack channel for it?
Thanks for your interest in our project! The first steps would be to download and explore the Allen Brain Observatory data. And to set up a development environment to run DataJoint Element Calcium Imaging. Before you begin, let’s meet virtually to discuss the project (scheduling link).
I’m Kshitij Soni, a senior-year student at IIPE Visakhapatnam. I am a successful GSOC 2022 contributor at ENSEMBL-EBI. I have worked as well in research experience in deep learning, computer vision and image processing, semantic segmentation, NLP, and OCR domains. I have already explored the Allen Brain Observatory Data and looking forward to getting started with this project.