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2 changes: 1 addition & 1 deletion _sources/hardware/lasers.rst.txt
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For all of these reasons, we recommend the use of optically pumped semiconductor
lasers (OPSLs) for imaging. OPSLs are solid state lasers that use a diode to
optically pump a semiconductor gain medium which can be tuned to adjust the emission
wavelength of the laser. Importantly, OPSLs have a narrow linewidth (<10 pM), low M
wavelength of the laser. Importantly, OPSLs have a narrow line width (<10 pM), low M
:sup:`2` value, can modulate the laser on microsecond timescales, and achieve high
and stable emission powers.

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**COMPASS**
#####################

Biologists are increasingly transitioning
towards more complex assays that require volumetric imaging with high spatiotemporal
resolution. Whether it is a developing embryo, the formation of a cell-cell
immunological synapse, breast cancer organoids migrating through a 3D collagen
matrix, or cytoskeletal rearrangements in a polarized epithelial monolayer, these
biological processes can only be understood when non-invasively and quantitatively
evaluated in their entirety through time.
Biologists are increasingly transitioning towards more complex assays that require volumetric imaging with high spatiotemporal resolution. Whether it is a developing embryo, the formation of an immunological synapse, cancer migrating through a 3D collagen matrix, these biological processes can only be understood when non-invasively and quantitatively evaluated in their entirety through time.

To meet these growing demands, we aim to develop simplified optical systems that provide cutting-edge imaging performance while ensuring ease of assembly and accessibility. By leveraging precision-engineered, baseplate-mounted designs, we eliminate unnecessary degrees of freedom, making high-resolution light-sheet microscopy more robust, reproducible, and approachable for researchers across disciplines. Our goal is to create powerful yet modular imaging platforms that enable biologists to focus on discovery rather than instrument complexity, accelerating the adoption of advanced volumetric imaging techniques.

-----------

**Project Philosophy**
=========================

* Simple to assemble, high-performance, light-sheet microscopes.
* Highly optimized operation with **navigate** software.
* Simplified optomechanical design for ease of use and maintenance.
* Streamlined optoelectronics and control for robust and reliable operation.

- **High-performance, easy-to-assemble light-sheet microscopes** designed for broad accessibility.
- **Seamless integration** with **navigate** software for optimized operation and intelligent imaging workflows.
- **Precision-engineered optomechanical design** for ease of use, reproducibility, and low maintenance.
- **Streamlined optoelectronics and control architecture** for robust, reliable, and modular system operation.
- **Modular, adaptable platforms** that support future advancements in light-sheet microscopy.

.. note::

This project is under active development.
--------

.. warning::

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injuries that may arise from or be related to the use of **COMPASS**.
Users should be aware of these risks and agree to utilize **COMPASS** at their own risk.

--------

.. toctree::
:caption: Introduction
:maxdepth: 1
:maxdepth: 2

introduction/background
introduction/principles
introduction/nanospim
introduction/aslm
introduction/opm

.. toctree::
:caption: Design Principles
:maxdepth: 1
:maxdepth: 2

design_principles/required_software
design_principles/design_process

.. toctree::
:caption: Development
:maxdepth: 1
:maxdepth: 2

.. toctree::
:caption: Hardware Considerations
:maxdepth: 1
:maxdepth: 2

hardware/room_preparation
hardware/table
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.. toctree::
:caption: Physical Assembly
:maxdepth: 1
:maxdepth: 2

physical_assembly/physical_assembly

.. toctree::
:caption: Imaging with the System
:maxdepth: 1
:maxdepth: 2

imaging/imaging

.. toctree::
:caption: System Characterization
:maxdepth: 1
:maxdepth: 2

system_characterization/system_characterization

contributing/software_architecture

.. toctree::
:caption: Future Development
:maxdepth: 1

future/aslm
future/opm


**Authors**
============
**COMPASS** includes key contributions from numerous individuals, both past and present,
in `The Dean Lab <https://www.dean-lab.org>`_.
**COMPASS** includes key contributions from numerous individuals, both past and present, in `The Dean Lab <https://www.dean-lab.org>`_.

**Funding**
============
**navigate** is supported by the
`UT Southwestern and University of North Carolina Center for Cell Signaling
<https://cellularsignaltransduction.org>`_, a Biomedical Technology Development and Dissemination (BTDD)
Center funded by the NIH National Institute of General Medical Science (RM1GM145399), and
the `Center for Metastatic Tumor Imaging <https://www.metastasis-imaging.org>`_ program, a
Cellular Cancer Biology Imaging Research (CCBIR) program funded by the NIH National Cancer Institute (U54CA268072).
<https://cellularsignaltransduction.org>`_, a Biomedical Technology Development and Dissemination (BTDD) Center funded by the NIH National Institute of General Medical Science (RM1GM145399), and the `Center for Metastatic Tumor Imaging <https://www.metastasis-imaging.org>`_ program, a Cellular Cancer Biology Imaging Research (CCBIR) program funded by the NIH National Cancer Institute (U54CA268072).
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9 changes: 6 additions & 3 deletions _templates/custom_class.html
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<a href="../index.html" class="icon icon-home">
COMPASS
<img src="../_static/compass.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../introduction/background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/principles.html">Light-Sheet Microscopy Optical Principles</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/nanospim.html">NanoSPIM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/opm.html">OPM</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Design Principles</span></p>
<ul>
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<p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../system_characterization/system_characterization.html">System Characterization</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Future Development</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../future/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../future/opm.html">OPM</a></li>
</ul>

</div>
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<a href="../index.html" class="icon icon-home">
COMPASS
<img src="../_static/compass.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../introduction/background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/principles.html">Light-Sheet Microscopy Optical Principles</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/nanospim.html">NanoSPIM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/opm.html">OPM</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Design Principles</span></p>
<ul>
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<p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../system_characterization/system_characterization.html">System Characterization</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Future Development</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../future/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../future/opm.html">OPM</a></li>
</ul>

</div>
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<a href="../index.html" class="icon icon-home">
COMPASS
<img src="../_static/compass.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../introduction/background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/principles.html">Light-Sheet Microscopy Optical Principles</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/nanospim.html">NanoSPIM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/opm.html">OPM</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Design Principles</span></p>
<ul class="current">
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<p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../system_characterization/system_characterization.html">System Characterization</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Future Development</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../future/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../future/opm.html">OPM</a></li>
</ul>

</div>
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<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Compass V1 General Design Process" href="design_process.html" />
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<a href="../index.html" class="icon icon-home">
COMPASS
<img src="../_static/compass.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../introduction/background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/principles.html">Light-Sheet Microscopy Optical Principles</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/nanospim.html">NanoSPIM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/opm.html">OPM</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Design Principles</span></p>
<ul class="current">
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<p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../system_characterization/system_characterization.html">System Characterization</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Future Development</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../future/aslm.html">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="../future/opm.html">OPM</a></li>
</ul>

</div>
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</div>
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<link rel="index" title="Index" href="../genindex.html" />
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<link rel="next" title="OPM" href="opm.html" />
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</a>
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<p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<li class="toctree-l1"><a class="reference internal" href="background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="principles.html">Light-Sheet Microscopy Optical Principles</a></li>
<li class="toctree-l1"><a class="reference internal" href="nanospim.html">NanoSPIM</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="opm.html">OPM</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../introduction/background.html">Why Light-Sheet Microscopy?</a></li>
<li class="toctree-l1"><a class="reference internal" href="../introduction/principles.html">Light-Sheet Microscopy Optical Principles</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Design Principles</span></p>
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<p class="caption" role="heading"><span class="caption-text">System Characterization</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../system_characterization/system_characterization.html">System Characterization</a></li>
</ul>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">ASLM</a></li>
<li class="toctree-l1"><a class="reference internal" href="opm.html">OPM</a></li>
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