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Update README.md (#125)
Updating the README with copy from docs website and providing a link to the documentation. --------- Co-authored-by: Nathan Clack <[email protected]>
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README.md

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[![DOI](https://zenodo.org/badge/632689876.svg)](https://zenodo.org/badge/latestdoi/632689876)
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[![Chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://acquire-imaging.zulipchat.com/)
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# acquire-imaging
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# Acquire
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This python package provides a multi-camera video streaming library focusing
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on performant microscopy.
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```bash
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python -m pip install acquire-imaging
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```
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Acquire ([`acquire-imaging` on PyPI](https://pypi.org/project/acquire-imaging/)) 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](https://napari.org/stable/).
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> **Note** This is an early stage project. If you find it interesting please
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> **Note** This is an early stage project. If you find it interesting, please
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> reach out!
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Support for:
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Acquire supports the following cameras (currently only on Windows):
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- Up to two independent video streams
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- Camera support:
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- Hamamatsu Orca Fusion BT (C15440-20UP) (windows only)
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- Vieworks VC-151MX-M6H00
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- Streaming file format support:
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- Tiff
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- Zarr v2
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- [Hamamatsu Orca Fusion BT (C15440-20UP)](https://www.hamamatsu.com/eu/en/product/cameras/cmos-cameras/C15440-20UP.html)
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- [Vieworks VC-151MX-M6H00](https://www.visionsystech.com/products/cameras/vieworks-vc-151mx-sony-imx411-sensor-ultra-high-resolution-cmos-camera-151-mp)
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- [FLIR Blackfly USB3 (BFLY-U3-23S6M-C)](https://www.flir.com/products/blackfly-usb3/?model=BFLY-U3-23S6M-C&vertical=machine+vision&segment=iis)
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- [FLIR Oryx 10GigE (ORX-10GS-51S5M-C)](https://www.flir.com/products/oryx-10gige/?model=ORX-10GS-51S5M-C&vertical=machine+vision&segment=iis)
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## Installation
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Acquire also supports the following output file formats:
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```bash
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python -m pip install acquire-imaging
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```
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- [Tiff](https://en.wikipedia.org/wiki/TIFF)
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- [OME-Zarr](https://ngff.openmicroscopy.org/latest/) for [Zarr v2](https://zarr.readthedocs.io/en/stable/spec/v2.html)
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- [Zarr v3](https://zarr.readthedocs.io/en/stable/spec/v3.html)
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## Usage
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See the tests for more examples.
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The provided [napari][] plugin is a good example of how to stream for visualization.
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For testing and demonstration purposes, Acquire provides a few simulated video sources.
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### List devices
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## Usage
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```python
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import acquire
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print(acquire.Runtime().device_manager().devices())
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```
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Check out our documentation [here](https://acquire-project.github.io/acquire-docs/).
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### Finite triggered acquisition
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```python
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import acquire
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runtime = acquire.Runtime()
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dm = runtime.device_manager()
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props = runtime.get_configuration()
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# select the first Hamamatsu camera
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props.video[0].camera.identifier = dm.select(acquire.DeviceKind.Camera, "hamamatsu.*")
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# stream to zarr
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props.video[0].storage.identifier = dm.select(acquire.DeviceKind.Storage, "zarr")
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props.video[0].storage.settings.filename = "out.zarr"
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props.video[0].camera.settings.shape = (2304, 2304)
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props.video[0].camera.settings.pixel_type = acquire.SampleType.U16
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props.video[0].max_frame_count = 100
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props = runtime.set_configuration(props)
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runtime.start()
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runtime.stop() # wait for acquisition to complete
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```
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The provided [napari](https://napari.org/stable/) plugin ([code here](https://github.com/acquire-project/acquire-python/blob/main/python/acquire/__init__.py#L131)) is a good example of how to stream for visualization.
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# Development
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## Development
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We welcome contributors. The following will help you get started building the
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code.
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## Environment
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### Environment
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Requires
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conda activate acquire
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```
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## Build
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### Build
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```bash
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conda activate acquire
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These values can be set to a specific version, or to `nightly` for nightly builds.
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## Develop
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### Develop
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```bash
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pip install -e ".[testing]"
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pre-commit install
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```
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## Troubleshooting
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### Troubleshooting
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### Maturin can't find a python interpreter
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#### Maturin can't find a python interpreter
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`Maturin` is a command line tool associated with
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[`pyo3`](https://pyo3.rs/v0.16.4/). It helps automate the build and packaging
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It seems to happen less frequently when invoked via pip - `pip install -e .`
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will end up invoking maturin.
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### Working with an editable install, how do I update the build?
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#### Working with an editable install, how do I update the build?
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It depends on what you changed:
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- **acquire-video-runtime** (c/c++ code): `touch wrapper.h; maturin develop`
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- **rust code**: `maturin develop`
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### Zarr V3 tests are failing
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#### Zarr V3 tests are failing
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You should make sure that the following environment variables are set:
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