This repository provides acquisition software for the expansion-assisted selective plane illumination microscope (ExA-SPIM).
Note
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. eLife 12:RP91979 https://doi.org/10.7554/eLife.91979.2
- Python: >=3.10, <=3.11 (tested)
- We using a virtual environment:
- For control of some specific devices, you will need the appropriate SDK installed:
This control software can optionally check I/O bandwidth to a local and externally networked drive location. This requires fio to be installed. For Windows, please install the correct binary files.
Important
The ExA-SPIM system operates at data rates up to 1.8 GB/sec. Datasets can also be multiple terabytes. Therefore it is recommended to have a large M.2 or U.2/3 NVME drive for data storage.
Important
Each raw camera is 288 megapixels (14192x10640 px). Live streaming therefore requires on-the-fly generation of multiple resolutions for each raw camera frame at high speed. This repository computes this pyramid using a GPU. Therefore it is recommended to have a decent GPU with at least 16 GB of RAM (i.e. NVIDIA A4000 or above).# New Document
Warning
By factory default, the Vieworks VP-151MX (or other model) cameras have firmware enablewd dark signal non-uniformity (DSNU) correction enabled. This results in non-uniform background pattern for lower light level imaging (i.e. fluorescence microscopy). This can be disabled by Vieworks over a remote support session by contacting [email protected]
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Create a virtual environment and activate it: On Windows:
conda create -n exaspim-control conda activate exaspim-control
or
python -m venv exaspim-control .\exaspim-control\Scripts\activate
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Clone the repository:
git clone https://github.com/AllenNeuralDynamics/exaspim-control.git && cd exaspim-control
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To use the software, in the root directory, run:
pip install -e .
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To develop the code, run:
pip install -e .[dev]
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To install all dependencies including all optional device drivers, run:
pip install -e .[all]
- (coming soon)
Example configuration files for a real experimental system are provided:
And the code can be launched by running main.py
Files for a simulated microscope are also available.
If you encounter any problems or would like to contribute to the project, please submit an Issue on GitHub.
exaspim-control is licensed under the MIT License. For more details, see the LICENSE file.