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Getting Started
This page is the recommended starting route through ISETBio. The rest of the sidebar has more detail on the main objects and computations; each of those pages has text and code snippets showing how objects are set up and methods applied.
- Download ISETCam, a required dependency, and ISETBio, and add both to your Matlab path.
- ISETBio uses methods from the Statistics and Machine Learning, Image Processing, and Signal Processing Matlab toolboxes.
- No specific Matlab version is required; we aim to support releases from roughly the last three years on a best-effort basis.
We have found the GitHub Desktop application
effective for downloading and managing GitHub repositories; some of us like
Git Tower. From the command line, git clone
followed by periodic git pull is the simplest way to install and stay up
to date. If you want to develop extensively, consider forking the
repository. Toolbox Toolbox
is another option: once installed, tbUse('isetbio') installs and
configures ISETBio and its dependencies.
Rendering scenes from 3D descriptions additionally requires ISET3D and Docker; see 3D rendering. Most users can skip this unless they need it.
The best way to learn ISETBio is to run and read its tutorial scripts,
under
tutorials/ in
the main repository. Tutorials are organized by topic (cmosaic,
eyemovement, outersegment, oisequences, optics, mrgc, and more).
A good first script, and a quick check that your installation works, is
t_cMosaicBasic.m.
See Guided tutorials for a curated starting list.
The first time you run a tutorial that needs cone-mosaic or RGC-mosaic data, ISETBio downloads it automatically from the Stanford Digital Repository and caches it locally; see ISETBIO-data.
Once you're comfortable running tutorials, the sidebar's topic pages (scenes and stimuli, retinal image, cone mosaic, eye movements, RGC mosaics) explain the underlying models in more depth and link to further examples.
If you are contributing code, isetbioUnitTest runs the repository's core
unit suite; see Validation and the matlab-testing skill in
the ISETBio repository for details.
If you have suggestions about tutorials you would like to see - or that you would like to contribute - please let us know by opening an issue on the isetbio repository.