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ExA-SPIM control

Overview

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

Getting Started

Prerequisites

  • Python: >=3.10, <=3.11 (tested)
  • We using a virtual environment:
  • For control of some specific devices, you will need the appropriate SDK installed:
    • voxel:
      • Core drivers, microscope, and acquisition codebase
    • view:
      • Core GUI codebase

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.

Recommended Hardware

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]

Installation

  1. 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

  2. Clone the repository:

    git clone https://github.com/AllenNeuralDynamics/exaspim-control.git && cd exaspim-control

  3. To use the software, in the root directory, run:

    pip install -e .

  4. To develop the code, run:

    pip install -e .[dev]

  5. To install all dependencies including all optional device drivers, run:

    pip install -e .[all]

Documentation

  • (coming soon)

Usage

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.

Support and Contribution

If you encounter any problems or would like to contribute to the project, please submit an Issue on GitHub.

License

exaspim-control is licensed under the MIT License. For more details, see the LICENSE file.