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Brian Wandell edited this page Dec 28, 2016 · 59 revisions

The Image System Engineering Toolbox for Biology (ISETBIO) is a Matlab toolbox designed to facilitate, integrate and document vision science calculations. The tools enable you to compute from the scene radiance, through the optics, and into the front end (retina, and ultimately beyond) of biological visual systems.

Goals

Vision scientists have developed many precise computations and facts that characterize critical steps in vision. Implementing these computations can be complex. ISETBIO is an open-source implementation that includes many such computations. We aim to provide them in a convenient and extensible format, and we hope ISETBIO enables investigators to build upon the vision science knowledge captured in this code to develop new biological insights and theoretical ideas.

We further hope that ISETBIO will help specialists in different subfields to share their in this computational framework. Specialists working on one part of the system - say optics - can contribute code that can be used by people who are expert in a different part of the system - say the retina. By placing the knowledge of the vision science fields in a unified software environment, we believe that all vision scientists will be able to better see The Big Picture.

Limitations

This project is based on the idea that computational models that are approximately right and exist are preferable to models that are perfect and do not exist. We hope that our colleagues and students become comfortable with the idea that a specific computation that implements our best current understanding is better than no computation. To support this approach, it is important to specify the domain over which the calculations have been checked and to give some sense of the accuracy of the model over that domain. We try to indicate the stimulus compliance range and precision of computations, as best we can, throughout the code and in the documentation.

The ISETBIO code base is evolving and being checked by different individuals. We do our best to write validation tests for each of the components as well as system tests and regression tests. We have confidence in many of the critical routines, which have been independently implemented and produce the same results. Other routines are still being tested. We have tried to make the differences clear by comments in the code and on this wiki. We invite you to perform your own tests and to share the results with us.

Status

This project includes specifications of the scene radiance, optics and retinal irradiance, cone mosaic absorptions and photocurrent, retinal encoding, eye movements, and computational classifiers. The compliance range and precision of the scene and optics and absorptions are the most advanced, and our confidence declines as we dive deeper into the nervous system.

Our ambitions go beyond the current coverage. With more experience and feedback, we will decide how much further we can extend the scope of these computations. That's right LGN and V1, we're talking about you.

For more information, see [Tutorials](ISETBIO Tutorials) and [Architecture](ISETBIO Architecture)

Satellite ISETBIO repositories

Utility repositories

Related links