Neurodata Without Borders (NWB) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. The NWB standard covers over 60 data types. In tandem with the development of the data standard, we are also developing NWB Widgets (GitHub - NeurodataWithoutBorders/nwb-jupyter-widgets: Explore the hierarchical structure of NWB 2.0 files and visualize data with Jupyter widgets.), an extensible library of Jupyter widgets that allows researchers to navigate through the structure of NWB files and visualize specific data elements. Interactive visualization of these data allows researchers to explore the data, gain scientific insight, and check the data for errors and artifacts.
The goal of this project is to develop visualizations for data types that do not yet have visualizations and to enhance usability and scalability of existing visualizations. The first aim is to develop visualizations for videos of neural activity acquired through a microscope. The second aim is to develop interactive tools that would allow a user to navigate easily through the stages of data processing. Students should be proficient in Python and familiar with Jupyter, matplotlib, and plotly. Familiarity with Jupyter widgets or neuroscience is also helpful.
Lead mentor: Ben Dichter @bendichter Backup mentor: Ryan Ly @rly , Oliver Ruebel
I am currently a UG student and have prior experience with Python, Jupyter, ipywidgets and libraries like matplotlib and plotly. I liked the project idea and have a rough idea how can we implement the second aim of the project to develop an interactive tool that will help us to navigate through the stages of data processing. However I want someone to guide me for the first aim…as I am not completely grasping the idea.
Hi @Sagnik220! You sound like you have many relevant skills for this project. This would be the type of project where we would work closely with the student and work out specific goals for building these interactive tools based on the needs of specific neuroscience labs with specific data types, so no worries if the aims are not completely clear at this point.
So as the organizations are out sir I would like to discuss to work out on the goals. And I hope to prepare a good enough proposal for the project with the help of the mentors
Hi! @bendichter
I’m Anoushka Ramesh, a CS undergraduate from Amrita Vishwa Vidhyapeetham, Amritapuri, India. I’m quite familiar with Python, Java and tools like Jupyter notebooks. Lately, I’ve been also working with React/django. I also happen to be a member of amFOSS amfoss.in, a student run community of open source enthusiasts.
Neuroscience and different simulations of the brain have always fascinated me. I loved to learn about deep brain simulations concerning Parkinson’s disease and watched different Khan Academy videos about neuroscience in my free time.
I took a look at the NWB widgets and I got a basic understanding of how the visualisations worked. I’d love to dig deeper into this and work with you to develop end-to-end visualisation tools for these data types.
What be a good place to discuss about the work plan and goals about this project?
It sounds like you have some great experience for this project! Could you send me an email at ben.dichter (at) gmail.com? Do you have a github profile you can share with me?