acquire-imaging 0.3.0

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Acquire

python -m pip install acquire-imaging

Acquire (acquire-imaging on PyPI) provides high-speed, multi-camera, video streaming for up to 2 cameras and image acquisition with a programming interface for streaming video data directly to Python, cloud-friendly file formats, and visualization platforms, such as napari.

Note This is an early stage project. If you find it interesting, please reach out!

Acquire supports the following cameras (currently only on Windows):

• Hamamatsu Orca Fusion BT (C15440-20UP)
• Vieworks VC-151MX-M6H00
• FLIR Blackfly USB3 (BFLY-U3-23S6M-C)
• FLIR Oryx 10GigE (ORX-10GS-51S5M-C)
• Photometrics Prime BSI
• Photometrics Prime BSI Express

Acquire also supports the following output file formats:

• Tiff
• OME-Zarr for Zarr v2
• Zarr v3

For testing and demonstration purposes, Acquire provides a few simulated video sources.

Usage

Check out our documentation here.

The provided napari plugin (code here) is a good example of how to stream for visualization.

Development

We welcome contributors. The following will help you get started building the code.

Environment

Requires

• CMake 3.23+ (download page or via chocolatey)
• A C++20 compiler (Microsoft Visual Studio Community download page, or clang)
• Rust >= 1.75 (via rustup, see install page)
• conda (optional; via miniconda)
• libclang >= v5.0 (on windows via choco choco install llvm or, on osx, via brew brew install llvm)

It's strongly recommended you create a python environment for development

conda create --name acquire python=3.11
conda activate acquire

Build

conda activate acquire
git submodule update --init --recursive
pip install maturin
maturin build -i python

Important When updating the 'acquire-video-runtime' (the c api), you need to manually trigger a rebuild by touching wrapper.h.

git submodule update # updates acquire-video-runtime
touch wrapper.h # will trigger a rebuild
python -m build

This package depends on a submodule (acquire-common) and binaries from the following Acquire drivers:

• acquire-driver-hdcam
• acquire-driver-egrabber
• acquire-driver-zarr
• acquire-driver-spinnaker
• acquire-driver-pvcam

The build script will automatically try to fetch the binaries from GitHub releases. In order to configure which release of each driver to use, you can set the value in drivers.json:

{
  "acquire-driver-hdcam": "0.1.0",
  "acquire-driver-egrabber": "0.1.0",
  "acquire-driver-zarr": "0.1.0",
  "acquire-driver-spinnaker": "0.1.0",
  "acquire-driver-pvcam": "0.1.0"
}

These values can be set to a specific version, or to nightly for nightly builds.

Develop

pip install -e ".[testing]"
pytest -s --tb=short --log-cli-level=0

This project uses pre-commit to run required checks as git hooks.

pip install pre-commit
pre-commit install

Troubleshooting

Maturin can't find a python interpreter

Maturin is a command line tool associated with pyo3. It helps automate the build and packaging process. It's invoked by setuptools during a build.

1. Double-check you've activated the right conda environment.
2. Try maturin build -i python

This seems to happen on windows in anaconda environments when multiple python interpreters are available on the path.

It seems to happen less frequently when invoked via pip - pip install -e . will end up invoking maturin.

Working with an editable install, how do I update the build?

It depends on what you changed:

• acquire-video-runtime (c/c++ code): touch wrapper.h; maturin develop
• rust code: maturin develop

Zarr V3 tests are failing

You should make sure that the following environment variables are set:

ZARR_V3_EXPERIMENTAL_API: 1
ZARR_V3_SHARDING: 1