A MATLAB-based microscopy control system for automated imaging experiments, built on top of Micro-Manager.
Scope is a comprehensive microscopy automation framework that provides high-level control over microscope hardware, fluidics systems, and imaging protocols. It's designed for complex imaging experiments including multi-channel fluorescence imaging, time-lapse studies, and automated fluidics control.
- MATLAB (R2018b or later recommended)
- Micro-Manager - Download from micro-manager.org
Scope requires Micro-Manager to be properly installed and configured. Please visit micro-manager.org to:
- Download the latest version of Micro-Manager
- Follow the installation instructions for your operating system
- Configure your microscope hardware through Micro-Manager's Hardware Configuration Wizard
- Ensure Micro-Manager is working with your specific microscope setup before using Scope
Note: Scope is designed to work with Micro-Manager 2.0 and later versions.
- Clone or download this repository to your local machine
- Add Scope to MATLAB path:
addpath(genpath('/path/to/Scope')); - Verify Micro-Manager connection:
% Test basic Micro-Manager connectivity mmc = mmcore.CMMCore; mmc.loadSystemConfiguration();
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Choose your microscope configuration:
% Available scope configurations Scp = NinjaScope; % For NinjaScope setup Scp = FutureScope; % For FutureScope setup Scp = OrangeScope; % For OrangeScope setup % ... and others
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Set up basic parameters:
Scp.Username = 'YourName'; Scp.Project = 'YourProject'; Scp.Dataset = 'YourExperiment';
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Configure imaging parameters:
% Set up acquisition data Scp.FlowData.AcqData = AcquisitionData; Scp.FlowData.AcqData(1).Channel = 'DeepBlue'; Scp.FlowData.AcqData(1).Exposure = 10;
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Start imaging:
Scp.acquire(Scp.FlowData.AcqData);
- Multi-scope support: Pre-configured setups for various microscope configurations
- Automated fluidics control: Integration with fluidics systems for automated protocols
- Advanced autofocus: Hardware and software-based autofocus capabilities
- Position management: Automated position creation and management
- Multi-channel imaging: Support for complex multi-channel acquisition protocols
- Time-lapse imaging: Automated time-series acquisition
- Data management: Organized data storage with metadata tracking
Check the Examples/ directory for complete working examples:
example_imaging.m- Basic imaging workflowexample_merfish_imaging.m- MERFISH imaging protocolexample_smfish_imaging.m- smFISH imaging protocoltest_timelapse.m- Time-lapse imaging example
Scope uses configuration files stored in the Configs/ directory. Each microscope setup has its own configuration file that defines:
- Hardware device mappings
- Channel configurations
- Camera settings
- Stage and objective parameters
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Micro-Manager not found: Ensure Micro-Manager is properly installed and the MATLAB path includes the Micro-Manager installation directory.
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Hardware connection errors: Verify your Micro-Manager hardware configuration is working before using Scope.
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Permission errors: Ensure you have write permissions to the data directory.
- Check the example scripts in the
Examples/directory - Review the configuration files in
Configs/for your specific microscope setup - Ensure Micro-Manager is working independently before using Scope
This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.
Contributions are welcome! Please feel free to submit pull requests or open issues for bugs and feature requests.
- Built on top of Micro-Manager
- Developed for the Wollman Lab at UCLA
- Supports various microscope configurations and imaging protocols
For questions and support:
- Check the example scripts and documentation
- Ensure Micro-Manager is properly configured
- Review the troubleshooting section above
- Open an issue on the project repository
Important: This software requires Micro-Manager to function. Please visit micro-manager.org for Micro-Manager installation and setup instructions.