scigantic-bil

Search the Brain Image Library and read its light-sheet, fMOST and STPT volumes over HTTP. No download, no account, no local copy.

import scigantic_bil as bil

cat = bil.BilCatalog.load()             # every BIL dataset, one 5 MB GET
for d in cat.light_sheet()[:5]:         # 808 light-sheet datasets, 278 TB
    print(d.bildid, d.contributor, d.species, f"{d.size_gb:.0f} GB")

img = bil.thumbnail("ace-bin-run")      # middle z-slice of a 27 GB stack, one 16 MB read

Installation

$ pip install scigantic-bil
$ pip install "scigantic-bil[zarr]"     # also open OME-Zarr stores in place

Why this exists

The Brain Image Library is the BRAIN Initiative's repository for whole-brain microscopy: 14,224 datasets and 6 PB as of its 2026-07-31 inventory, including the largest public collection of cleared-tissue light-sheet brains. Everything is served over plain HTTPS with directory listings and range requests, and the metadata API needs no key. That makes it readable in place, but nothing in the ecosystem did so.

BIL's own brainimagelibrary package (py-brain-sdk, 0.0.23, GPL-3.0) wraps the metadata API and downloads datasets, with resumable transfers and citation lookups. Its source (read, not assumed, on 2026-09-08) contains no image reading at all: the only route from a BIL id to pixels is DatasetInventory.download(), which fetches the files to disk. For a 27 GB light-sheet stack that is the whole stack, to look at one slice.

This package was then run against the archive rather than a handful of friendly datasets: random samples across every technique, the largest trees (4.7 million files), the largest single files (a 21.7 GB OME-TIFF, a 10 GB single-strip plane, 199 GB TIFFs), paths with # and spaces and non-ASCII characters, two-word and one-word dataset ids, stale inventory paths, landing-zone paths, and sixteen threads on a cold cache. What that found is fixed and covered by tests; what it cannot read yet is stated below.

This package is the other half. It reads BIL in place:

• A typed, in-memory catalog of the whole archive from BIL's daily inventory TSV, with structured filters and a light-sheet finder that unions the inventory's technique field with BIL's fulltext index. The technique field alone says light sheet for 348 datasets; the union finds 808. The rest are tagged other and only say light sheet in their abstract or instrument record.
• Single-slice TIFF reads straight from the download server. The dominant BIL layout is one TIFF per z-plane, about 16 MB each; one slice is one request.
• OME-Zarr stores opened lazily through zarr's HTTP store, with pyramid levels checked against what the server actually has (one BIL store declares eight levels and serves seven).
• Thumbnails that read as little as possible: the middle slice of a TIFF stack, or the coarsest level of a zarr pyramid.
• Bounded previews of files of any size. preview_plane() reads the coarsest pyramid level, or every k-th row by offset from an uncompressed plane, or a sample of strips, or a centre region of a tiled page. A 10 GB single-strip MERFISH mosaic previews from 63 MB of reads; asarray() would fetch all 10 GB.
• fMOST TeraFly trees (RES_<x>x<y>x<z>_/ folders, 985 datasets) previewed from the coarsest resolution folder, stitched. The full-resolution folder of one such brain holds 1.6 million files and is never listed.
• A seekable HTTP file object (HttpFile) so tifffile fetches only the IFDs, pages, tiles or regions you ask for from a large TIFF, with read_region() for a rectangle of a tiled page.
• BIL's per-dataset manifest (path, size, MD5, URL for every file) as one gzipped GET, so a deep tree lists in one request. Guarded by size: a 4.7 million file dataset's manifest is 710 MB gzipped, and walk() crawls instead of downloading that.

Measured on 2026-09-08 from a residential connection, against the live archive:

Bulk transfers are sequential because parallel streams measured slower. Sampling reads (rows 20 MB apart, TeraFly blocks) are latency-bound and go through a small pool: 512 sequential range requests took 68 s for 63 MB, eight workers take a few seconds.

Dependencies are requests, numpy, tifffile, imagecodecs (LZW and Deflate strips are common in BIL TIFFs) and pillow (a second decoder for ImageJ Deflate stacks that libdeflate rejects). zarr and pandas are extras.

Data license

BIL data is distributed under CC BY-SA 4.0; some datasets additionally carry the Allen Institute Terms of Use, recorded per dataset in DatasetDetail.rights. This package's code is MIT-0. The permissive code license does not extend to the data: anything you derive from BIL images and redistribute needs attribution and the same license. Cite the dataset's DOI (DatasetDetail.doi) and its publications (DatasetDetail.publications).

Catalog

cat = bil.BilCatalog.load()                     # newest daily inventory
cat = bil.BilCatalog.load(date="20260731")      # a specific snapshot
len(cat), cat.date                              # (14224, '20260731')

cat.summary()                                   # datasets, files, TB, top modality/technique/species/extensions
cat["ace-cup-eel"]                              # one Dataset by id
cat.filter(technique="fMOST", species="mouse")  # case-insensitive substring match, any combination
cat.filter(extension=".swc")                    # datasets shipping neuron reconstructions
cat.filter(max_size_gb=2)                       # small enough to pull whole
cat.search("iDISCO")                            # BIL's fulltext index, joined to inventory rows
cat.light_sheet()                               # technique field + fulltext, deduplicated
cat.to_dataframe(cat.filter(technique="STPT"))  # pandas, with pip install "scigantic-bil[pandas]"

A Dataset carries what the inventory indexes: contributor, affiliation, award, project, consortium, modality, technique, species, genotype, file count, size, and a per-extension file histogram (extensions). Dataset.url is the dataset's root on the download server.

Metadata

The full record lives on the metadata API and is fetched on demand:

d = bil.retrieve("ace-cup-eel")
d.title, d.abstract, d.rights_identifier        # 'Light-sheet imaged brain ...', ..., 'CC-BY-SA-4.0'
d.microscope_type, d.species                    # 'Light-sheet', 'mouse'
d.instrument                                    # {'microscopetype': 'Light-sheet', 'microscopemanufacturerandmodel': 'Zeiss Z.1', ...}
d.specimen, d.images                            # specimen record; per-image axes, step sizes, channels
d.contributors, d.publications, d.funders
d.is_light_sheet                                # checks technique, instrument and free text together

bil.retrieve_many(["ace-cup-eel", "ace-bin-run"])   # batched POST, unknown ids dropped
bil.fulltext("CLARITY")                             # BIL ids only
bil.query("specimen", species="mouse")              # one structured element=value pair

Structured queries match exactly (query("instrument", microscopetype="Light-sheet") found 6 datasets on 2026-09-08 where fulltext("light sheet") found 777), so use fulltext for discovery and the catalog's filters for structure.

Files

bil.list_files("ace-bin-run")            # one directory: name, size, modified, url
bil.manifest("ace-bin-run")              # every file, with relative path and MD5, one gzipped GET
list(bil.walk("ace-cup-eel"))            # recursive; a zarr store appears once, as a directory
bil.find("ace-bin-run", suffix=".tif")   # natural sort, so Z00002 follows Z00001
bil.find_zarr("ace-cup-eel")             # ['https://download.brainimagelibrary.org/.../subject_5.zarr/']
bil.download(entry, "out/")              # the one function that writes image bytes to disk

Any of these accept a BIL id, a Dataset, a /bil/data/... path from the metadata, or a download-server URL. Paths are percent-encoded for you: 39 inventory paths carry spaces, # or non-ASCII characters, and an unencoded # is a URL fragment. Two things the inventory gets wrong are reported rather than hidden: a directory renamed on the server since the inventory was built (the error names the parent to list) and a dataset still under BIL's landing zone, which is not public.

Images

stack = bil.slices("ace-bin-run")        # 1,923 FileEntry in z order, nothing fetched yet
img = bil.read_tiff(stack[961])          # (4501, 3828) uint16, one request
vol = bil.read_stack("ace-bin-run", start=900, stop=960, step=10)   # (6, 4501, 3828)
bil.thumbnail("ace-bin-run", max_size=512)                          # middle slice, stride-downsampled
bil.thumbnail("ace-bin-run", index=100, channel="ch02")

Previews of large files

bil.tiff_info(entry)                     # pages, shape, dtype, tiled, pyramid levels, from the IFDs only
bil.preview_plane(entry, max_size=512)   # bounded read whatever the file size, see the table above
bil.read_region(entry, rows=(16000, 18048), cols=(7000, 9048), page=0)   # tiles covering a rectangle, [zarr] extra
bil.terafly_levels("ace-cap-cop")        # [((793, 1268, 350), url), ...] coarsest first, for fMOST trees
bil.terafly_thumbnail("ace-cap-cop")     # one stitched plane through the middle of the coarsest level
bil.first_images("ace-owl-cot")          # the first folder of TIFFs by bounded descent, never a crawl

thumbnail() tries these in order: a TeraFly tree, an OME-Zarr store, then the first folder of TIFFs. It never lists a whole tree; the unbounded version sat on a 1.6 million file fMOST dataset for over twenty minutes before the bound existed.

What it does not read

Formats this package does not decode raise UnsupportedFormatError naming what does. Across the archive's techniques the big one is JPEG 2000 (.jp2, 5,787 datasets: most STPT sections, viral tracing and enhancer-labelling brains): download() then glymur. Also Imaris .ims (HDF5, h5py), NIfTI (nibabel), MERFISH .dax frames (raw uint16, numpy), SWC morphologies (navis), and tables (pandas). Reading .jp2 in place is the obvious next addition; the format has resolution levels built in, so a preview should not need the whole file.

OME-Zarr

g = bil.open_zarr("ace-cup-eel")         # lazy; nothing read until sliced
bil.zarr_levels(g)                       # ['0', ..., '6'], as served, not as declared
g["6"][0, 0, 400]                        # one plane of the coarsest level, a few chunks
bil.zarr_thumbnail(g, max_size=512)

A zarr store is a directory, so it never shows in the inventory's extension histogram; find_zarr() is how to know a dataset ships one. Requires pip install "scigantic-bil[zarr]" (zarr 3, fsspec, aiohttp) and Python 3.11 or newer, which is zarr 3's own floor; on 3.10 the extra installs nothing and open_zarr() raises a clear ImportError.

Caching

On by default. Metadata responses, directory listings and manifests are cached to ~/.cache/scigantic-bil (macOS: ~/Library/Caches/scigantic-bil; override with SCIGANTIC_BIL_CACHE or enable_cache(cache_dir=...)) and expire after 7 days, since BIL republishes its inventory every few days. Inventory snapshots are immutable once published and are kept as plain TSV files without expiry. Image bytes are never cached.

bil.disable_cache()
bil.enable_cache(ttl_days=1)
bil.clear_cache()

Command line

$ scigantic-bil summary
$ scigantic-bil light-sheet --limit 20
$ scigantic-bil search "iDISCO" --json
$ scigantic-bil filter --technique fMOST --species mouse --max-gb 100
$ scigantic-bil info ace-cup-eel
$ scigantic-bil files ace-bin-run --zarr
$ scigantic-bil thumbnail ace-bin-run slice.png --size 512

Testing

Every test runs live against BIL, no mocks, the same philosophy as the rest of the scigantic-* packages. The suite takes one to two minutes depending on the server and includes the stress cases above: the 21 GB OME-TIFF, the 10 GB plane, the # path, the 4.7 million file manifest guard, the TeraFly tree, the Pillow fallback, six threads loading the catalog cold. CI runs Python 3.10 through 3.14 plus mypy --strict.

License

MIT-0 for the code. See Data license for the data.