GSoC 2023 Project Idea 10.1 Developing reanalysis tools for Allen Brain Observatory data (350 h)

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:

  1. 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.
  2. DataJoint Elements: a growing compilation of community-curated, open-source software modules for building automated data pipelines and analysis workflows for neuroscience experiments.
  3. 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 :

  1. Develop mechanism to ingest Brain Observatory data into the Element.
  2. Demonstrate reanalysis of this data via jupyter notebook
  3. Add unit tests for the above mechanism.
  4. 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

Time commitment: Half-time or full-time (350 h)

Lead mentor: Dimitri Yatsenko, Kabilar Gunalan

Project website:

Backup mentors: Chris Brozdowski

Tech keywords: Python, Two-Photon Imaging, Reanalysis, Replication, MySQL

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?
Thank you

Hi @Viren_Varma,

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).

Thank you!


Sure Sure @kabilar Sir absolutely!, I’ve sent you the meet invite. I’ll go through the link and be prepared for it.

@Viren_Varma Sounds great, thanks!

Hello @dimitri @kabilar Sir!

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.

Hi, it’s a bit late but I’m really interested in contributing to this project. Can you please provide next steps in writing proposal. Thanks.

Hi @kshitijsoni and @MauryaRitesh,

Thank you for your interest in our project! In order to help you plan out your proposal, let’s meet individually to discuss the project (scheduling link).

Thank you!


Hello @kshitijsoni I have already explored the Allen Brain Observatory Data, and i’m so interested in contributing to this project. Can i get an opportunity to discuss this project with you? Thank you

Hi @Enoch_Adetunji,

Thanks for your interest in our project! I would be happy to discuss. Applicant proposals are due on April 4th. In order to help you plan out your proposal, we can meet virtually (scheduling link).

Thank you!


Alright. Thank you, i’ll be happy to discuss further with you

Hello sir, firstly I would like to say I am very sorry for the late message I have been in the hospital for the last month. I would like to work on your project, I have viewed the Allen Brain observatory data and I am highly intrigued by it. I would like to contribute to your project and I will be highly obliged if you consider me. I have previously done some work in natural language processing and computer vision and I am a very paced learner of new things. I am currently in my 3rd year at IIT Kanpur pursuing a major in Chemistry and minor in Statistics and Data Science. Hope to hear from you soon. Thank You

Hi @kabilar , I’m an MS (by Res.) student at IIIT Hyderabad working on Computational Neuroscience. I have worked on a mouse visual cortex dataset from the Allen Brain Observatory for our group project during NeuroMatch Academy 2022.

As of now, I have one paper under review at Interspeech 2023. In it, I studied the neural mechanisms underlying auditory perception using an openly available dataset from CRCNS. I have previously been a TA for an advanced programming course on Data Structures and Algorithms. I have also worked on research projects on Computer Vision and Natural Language Processing, using tools such as PyTorch, Keras, and TensorFlow. I’m also familiar with Bash.

I’m interested in this project. I know it’s very late but can we schedule a meeting to draft a proposal?

Hi @Aditya_Sharma and @Kumar_Neelabh,

Thank you for your interest in our project! I unfortunately did not have availability to meet before the deadline to submit the proposals. If you are available, we look forward to your participation in GSoC in 2024, and would welcome your contributions to these open source projects at any time.

Thank you.


Hello sir,
Sure i would love to work on the project from now only as it would like to help me build a solid background and understand the structure in a better way for when I apply for gsoc in 2024. Sir will you please guide me the further steps as to how I should contribute.

Thank you
Aditya Sharma.