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Project description
akuire
Akuire is a prototype of asynchronous acquisiton engine for smart-microscopy workflows. It was designed during the "Smart Microscopy" hackathon at the Lund Bioimaging Center.
The main goal of Akuire is to provide a simple and flexible way to acquire images from a microscope in an asynchronous way, interfacing with different microscopy software backbones.
Installation
To install Akuire, you can use pip:
pip install akuire
Usage
To use Akuire, you need to create an instance of the AcquistionEinge
class, passing the desired device managers and the system settings.
You can use the acquisition engine to acquire images from the microscope through predefined plans in an Acquisition
object.
from akuire import AcquisitionEngine, Acquisition, MoveEvent, AcquireZStackEvent, SystemConfig
from akuire.managers.testing import NonSweepableCamera, ZStageManager, VirtualStageManager
import asyncio
engine = AcquisitionEngine(
system_config=SystemConfig(
managers={
"virtual_camera": NonSweepableCamera(),
"virtual_z_stage": ZStageManager(),
"virtual_stage": VirtualStageManager(),
}
),
compiler=compile_events,
)
x = Acquisition(
events=[
MoveEvent(x=1, y=2),
AcquireZStackEvent(z_steps=30, item_exposure_time=0.1),
]
)
# The acquisition plan is compiled into a list of events
async def main():
async with engine as e:
# A blocking operation that acquires the ZStack
# The event plan will be "compiled" into a list of events
# that are compatible with the underlying hardware
# trying to optimize the acquisition process
result = await e.acquire(x)
# result is a ZStack object
# A hyperstack can be created from the ZStack object
stack = result.to_z_stack()
if __name__ == "__main__":
asyncio.run(main())
Documentation
Right now this is the only documentation available. More documentation will be added in the future. If you are interested in potential use cases, please check the examples folder.
Contributing
Pull requests are welcome. Happy for any feedback or suggestions.
License
This project is licensed under the MIT License - see the LICENSE file for details.
Project details
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