AcqStore¶
AcqStore is a Python package for acquisition-backed microscopy files: discovery, loading, ROIs, metadata, and quantitative analysis of line-scan kymographs.
An acquisition-backed file is more than pixels. AcqStore keeps acquisition context with the recording. That includes format-specific header and calibration, optional ROIs, and analysis sidecars. Scripts and notebooks share one scientific backend.
AcqStore uses lazy loading for image pixels and large analysis CSV tables. You can browse many files without loading every pixel array into memory. See Loading an image.
One example GUI that uses AcqStore is CloudScope. AcqStore itself does not depend on that application.
Current quantitative analysis workflows target line scan kymographs:
- blood flow velocity (Radon transform)
- vessel diameter
- sum intensity / peak detection for functional reporters (like GCaMP)
- heart rate derived from velocity results
Start here¶
- Install
- Sample data
- Loading an image
- AcqImage: header metadata, pixels, ROIs, analysis, sidecars
- ROIs
- Analysis
Quick start¶
from acqstore.acq_image.acq_image_list import AcqImageList
lst = AcqImageList('/path/to/folder', folder_depth=2)
Supported file formats¶
Commercial microscopy formats:
- Olympus / Evident
.oir - Zeiss
.czi - Nikon
.nd2
Open image formats:
- TIFF
.tif - OME-Zarr
.ome.zarr
See Loading an image for how loaders work, including the native
.cs.ome.zarr format (in development).
API reference¶
mkdocstrings-generated pages for AcqImage, analyses, pools, and batch APIs: