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The Image System Engineering Toolbox for Biology - ISETBio - is a Matlab toolbox for calculating the properties of the front end of the visual system. The toolbox begins with a description of the scene radiance, how the radiance is transformed by the optics into the retinal image, captured of light by the photopigment, the photocurrent responses in the receptors. We are actively working on modeling how the photoreceptor signals are converted into retinal ganglion cell responses.

This repository includes a WIKI that describes the software as well as many examples of how to perform computations to calculate the visual encoding of light in the eye. The WIKI also describes tools to quantify, view and and analyze the information contained at different neural stages.

As of May 27, 2024 To run ISETBio, you must download ISETCam and have it on your Matlab path. See installing ISETCam.

History

  • May 29, 2024 - See changes to ISETCam in the ReadMe for that repository. The validation routines for ISETBio have been moved into a new ISETValidations repository.

Ancient history

The ISETBIO code includes a portion of Image Systems Engineering Toolbox (ISET) that is sold by Imageval Consulting, LLC. That code is designed to help industrial partners design novel image sensors. The ISETBIO portion of the ISET code is freely distributed for use in modeling image formation in biological systems.

ISETBIO also includes the WavefrontOptics code developed by David Brainard, Heidi Hofer and Brian Wandell. That code implements methods for taking adaptive optics data from wavefront sensors and calculating the optical blur as a function of wavelength for model human eyes. The toolbox relies on data collected by Thibos and colleagues. We also gratefully acknowledge important contributions from Jon Winawer.

isetbio's Projects

ejlexperimentalrgc icon ejlexperimentalrgc

Run simulations in isetbio loading in RGC mosaics with parameters fitted from experimental data in the Chichilnisky Lab.

ejlfigurereproduction icon ejlfigurereproduction

Reproduces figure 2 from Heitman, Brackbill, ..., Chichilnisky, et al., 2016 on the failure of the GLM to predict RGC responses to natural scene stimuli.

ejlphosphene icon ejlphosphene

A simulation of the responses of RGCs to stimulation by an electrode array and reconstruction of the perceived phosphenes.

exampletesttoolbox icon exampletesttoolbox

Code the will run all standard format examples in a source tree and keep track of which worked.

ibiocolordetectold icon ibiocolordetectold

An isetbio computational observer for threshold detection of color Gabor stimuli

isetbio icon isetbio

Tools for modeling image systems engineering in the human visual system front end

isetbio_v0.1 icon isetbio_v0.1

Tools for modeling image systems engineering in the human visual system front end

isetbiocsfgenerator icon isetbiocsfgenerator

Framework for the adaptive estimation of performance in ISETBio-modeled visual performance tasks

isetbioencoding icon isetbioencoding

Scripts for the figures in the Circadian rhythms/Spitschan chapter (Brian, David, Nicolas)

isetcore icon isetcore

The purpose of this module is to hold functions that are common between isetbio and isetcam, as submodules in each.

isetimagepipeline icon isetimagepipeline

Bayesian reconstruction analysis of the initial visual encoding, using ISETBio as the visual system model.

isetmacaque icon isetmacaque

Project that uses isetbio to model the retina of the macaque monkey

isetmarmoset icon isetmarmoset

Code to use ISETBio to characterize the eye of the marmoset

isetpipelinetoolbox icon isetpipelinetoolbox

Routines related to ISETImagePipeline project that may also be called from elsewhere

jwlorientedgabor icon jwlorientedgabor

Simulation of an experiment by Marisa Carrasco and Jon Winawer measuring orientation discrimination thresholds of an acrhomatic, peripheral Gabor

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