ISETBIO data

ISETBio data

ISETBio uses two kinds of data of its own: small reference data committed directly in the repository, and large retinal mosaic data fetched on demand from the Stanford Digital Repository (SDR). Scene/image data sets are ISETCam's responsibility; see below.

Repo-committed reference data

data/ (about 17 MB) holds small, static reference files that ship with every checkout and are always available, no download step required:

• data/datafiles/spectra/ - spectral basis functions and color-matching data
• data/datafiles/human/ - human lens, cone, and melanopsin spectral data, wavefront measurements (wvf/), blood vessel and macular data
• data/datafiles/optics/eccentricityvarying/ - eccentricity-varying optics data
• data/datafiles/mouse/, data/datafiles/treeshrew/ - non-human species data
• data/datafiles/bipolar/ - bipolar model parameters
• data/datafiles/ptbcal/ - Psychophysics Toolbox calibration files

This is distinct from the large retinal mosaic data below, both in size and in how it's obtained: it's git-tracked and present immediately, not downloaded on first use.

Three directories are deliberately empty placeholders for data you generate locally, each with a README explaining its role: data/datafiles/cones/lattices/, data/datafiles/rgc/lattices/, and ganglioncells/mosaics/ONmRGC/. A file you generate yourself (e.g., with retinalattice.generatePatch) lands in one of these and always takes precedence over anything downloaded from the SDR.

Retinal mosaic data (current)

Cone and midget-RGC mosaic data is no longer stored in the Git repository. It is published in the Stanford Digital Repository (SDR) as the isetbio-mosaics deposit (59 files, about 1.2 GB) and downloaded automatically the first time your code needs a given file.

% A precomputed cone mosaic: 0.5 x 0.5 degrees at the fovea
cm = mosaicLoad([0.5 0.5], [0 0]);

% See what the deposit publishes
mosaicLoad('list');

% Pre-baked ON-midget-RGC circuits
mRGCMosaic.listPrebakedMosaics();

Nothing special is required to use it - loading a mosaic works the way it always did. The first call for a given file pauses to download it; later calls read a verified, checksummed local copy cached under isetbio/data/sdr/isetbio-mosaics/ (git-ignored, so cached files are never committed).

The Remote Data Toolbox is no longer used for this data and should not be installed for this purpose.

For deposit contents, cache layout, checksum behavior, offline mirroring, and troubleshooting, see docs/sdr-mosaic-data.md in the isetbio repository.

Other data sets

Scene and image data sets (hyperspectral and multispectral natural scenes, HDR collections, and similar) are managed through ISETCam, using the same ieWebGet mechanism underneath. See the ISETCam wiki's data page.

Validation (ground-truth test) data is described with the current test runners; see Validation.