AcqStore¶
AcqStore is a Python package for loading, annotating, and analyzing acquisition-backed microscopy files. It provides the scientific backend used by applications such as CloudScope, as well as by notebooks and scripts.
Current quantitative analysis workflows are designed for line scan kymographs and include:
- blood flow velocity analysis using a Radon-transform-based method
- vessel diameter analysis
- peak detection / sum intensity analysis for functional fluorescence reporters (like GCaMP)
- heart rate analysis derived from velocity results
Install¶
git clone https://github.com/mapmanager/acqstore.git
cd acqstore
uv sync
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
Who is this documentation for?¶
-
Data Scientist
Understand
AcqImage,AcqImageList, line scan kymograph analysis, saved files, metadata, and notebook workflows. -
Developer
Clone the repository, run tests, build docs, and contribute to AcqStore.
-
API Reference
mkdocstrings-generated API pages for AcqImage, analyses, pools, and batch APIs.