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Sample data

AcqStore downloads reusable sample datasets from the cloudscope-data repository. The live catalog is:

https://raw.githubusercontent.com/mapmanager/cloudscope-data/main/catalog.json

Use acqstore.sample_data so docs, notebooks, and scripts share the same download/cache path.

List available samples

from acqstore.sample_data import list_samples

for sample in list_samples():
    kind = 'file' if sample.is_single_file else 'folder'
    print(f'{sample.name} ({kind}) - {sample.label}')

Download and load a single-file sample

Some catalog entries hold one representative recording. For those, ensure_sample_file(id) returns the path to open with AcqImage:

from acqstore.acq_image import AcqImage
from acqstore.sample_data import ensure_sample_file

acq = AcqImage(str(ensure_sample_file('kymograph-flow')))
print(acq.name, acq.path)

Current single-file IDs:

  • kymograph-flow: one OIR line-scan kymograph (velocity / heart rate demos)
  • kymograph-diameter: one TIFF line-scan kymograph (diameter / sum intensity demos)

ensure_sample_file raises SampleDataError for a folder sample. Use ensure_sample + AcqImageList for those. The returned path is usually a regular file (.oir, .tif, …). It can also be a directory-backed store such as *.ome.zarr, which AcqImage opens like any other supported path.

Download and load a folder sample

ensure_sample(id) downloads (if needed), extracts, and returns a folder path suitable for AcqImageList:

from acqstore.acq_image import AcqImageList
from acqstore.sample_data import ensure_sample

folder = ensure_sample('velocity-sample-data')
acq_list = AcqImageList(str(folder))
print(len(acq_list), 'files')

Current folder IDs:

  • velocity-sample-data: OIR line-scan kymographs for velocity / heart rate
  • diameter-sample-data: TIFF line-scan kymographs for diameter / sum intensity

Use folder samples for batch notebooks and multi-file workflows.

Cache location

By default, archives land under the platform user-data directory for acqstore / sample-data (on macOS typically ~/Library/Application Support/acqstore/sample-data).

Override the root with the environment variable CLOUDSCOPE_SAMPLE_DATA_DIR.

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