59 lines
2.3 KiB
Markdown
59 lines
2.3 KiB
Markdown
<h1 align="center">
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<img src="https://github.com/TheDeanLab/navigate/blob/develop/src/navigate/view/icon/mic.ico?raw=true" />
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navigate
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<h2 align="center">
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open source light sheet microscope control
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</h2>
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</h1>
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[](https://github.com/TheDeanLab/navigate/actions/workflows/push_checks.yaml)
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[](https://codecov.io/gh/TheDeanLab/navigate)
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**navigate** is an open source Python package for control of light-sheet microscopes.
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It allows for easily reconfigurable hardware setups and automated acquisition routines.
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### Quick install
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Download and install [Miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links).
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```
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conda create -n navigate python=3.9.7
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conda activate navigate
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pip install git+https://github.com/TheDeanLab/navigate.git
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```
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To test, run `conda activate navigate` and launch in synthetic hardware mode with `navigate
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-sh`. Developers will have to install additional dependencies with
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`pip install -e '.[dev]'`.
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### Documentation
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Please refer to and contribute to the documentation, which can be found on GitHub Pages: [https://thedeanlab.github.io/navigate/](https://thedeanlab.github.io/navigate/).
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### Command Line Arguments
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Below are the optional arguments that can be passed to the navigate software:
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- `-h, --help`
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Provides information on the optional arguments that can be passed to **navigate**.
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- `-sh, --synthetic_hardware`
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Open the software without any hardware attached for testing
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and setting up a new system.
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- `-c, --configurator`
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Open the **navigate** configuration wizard, which provides a
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graphical interface for setting up the hardware configuration.
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- `-d`
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Enables the debugging menu in the software.
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- `--config-file`
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Pass a non-default `configuration.yaml` file to **navigate**.
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- `--experiment_file`
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Pass a non-default `experiment.yaml` file to **navigate**.
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- `--gui-config-file`
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Pass a non-default `gui_config.yaml` file to **navigate**.
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- `--waveform-constants-file`
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Pass a non-default waveform constants file to **navigate**.
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- `--rest_api_file`
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Pass a non-default REST API file to **navigate**.
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- `--logging_config`
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Pass a non-default logging configuration file to **navigate**.
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