Software – Cloud scale collaborative science

The Simons Foundation generously supported the development of software for scientific data management.  The initial concepts and implementation that were developed at Stanford in the CNI are now being developed and extended for use at other sites by a commercial venture,  An example of the project, along with the nice artwork from Laura Jacobson, is presented on the Google Customers page.

In the Videos section of my web pages, you can find two talks about the project.

The software developed in this project is also being used by Russ Poldrack and his colleagues as a database backend to support their work on open data sharing in openNeuro.  And Flywheel has implemented the BIDS format into their product.  Collaboration!

Open source and free software projects

Members of the lab (and I) maintain various MR physics and engineering tools in several github accounts. These include

  • ISETCAM - (image systems engineering toolbox for cameras).  This project includes a set of repositories to support camera design and analysis.  This includes the modern implementation of S-CIELAB (1998) image quality metric.  The tools here were the basis of the company, Imageval, which supported the development of CMOS imagers at more than 80 companies around the world.
  • ISETBIO  - (image systems engineering toolbox for biology). This project includes a set of repositories to model of the front end of the human visual system, from scene radiance to retinal ganglion cell responses.  This is a very active project in collaboration with Brainard and Cottaris at U. Penn.  How is the modeling going?  We are part of the way there, and I am very excited!
  • VISTASOFT  – This project includes methods for analyzing fMRI, diffusion weighted imaging, anatomical data, and ECoG data. Over the last twenty years, many people have contributed to this repository (Steve Engel, Alex Wade, Bob Dougherty, Franco Pestilli, Alyssa Brewer, Jon Winawer, Jason Yeatman, Ariel Rokem, Dora Hermes, Dave Heeger, Geoff Boynton).  Over the last few years Jon Winawer and his team have been the most active group maintaining and extending the software. I hope to get back to working on it before long.


These are now mostly managed through the software projects and links on the wiki pages above.  I am leaving these here for now.