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Repositories
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This section groups lab software, hardware, and publication-linked repositories.

Projects
========

These repositories capture core software and hardware efforts from the lab.

- `navigate <https://thedeanlab.github.io/navigate/>`_ - Light-sheet microscopy software packages for intelligent imaging of complex tissue samples.
- `Altair <https://thedeanlab.github.io/altair/>`_ - Cost-effective, easy-to-assemble, and performant light-sheet microscopes.
- `clearex <https://github.com/TheDeanLab/clearex>`_ - Open-source Dean Lab analysis resources on GitHub.
- `cyDPNI <https://github.com/TheDeanLab/CyDPNI>`_ - A Python package for analyzing sub-cellular polarization in fluorescence microscopy images.

.. _publications-home:

Publications
============

A list of our publications with links to the associated GitHub repositories. These repositories
contain the source code, data, and CAD files associated with the publication.  A comprehensive list of our publications can be found on our website at `www.dean-lab.org <www.dean-lab.org>`_, `Google Scholar <https://scholar.google.com/citations?user=Uv0B5xIAAAAJ&hl>`_, or `PubMed <https://www.ncbi.nlm.nih.gov/myncbi/kevin.dean.1/bibliography/public/>`_.

- `2015, Dean <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2015-dean>`_ - Deconvolution-free subcellular imaging with axially swept light sheet microscopy.
- `2016, Dean <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2016-dean>`_ - Diagonally scanned light-sheet microscopy for fast volumetric imaging of adherent cells.
- `2016, Welf <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2016-welf-meSPIM>`_ - Quantitative multiscale cell imaging in controlled 3D microenvironments.
- `2019, Chakraborty <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2019-chakraborty>`_ - Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution.
- `2020, Chang <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2020-chang-systematic-comparison>`_ - Systematic and quantitative comparison of lattice and Gaussian light-sheets.
- `2020, Sapoznik <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2020-sapoznik-oblique-plane-microscopy>`_ - A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics.
- `2021, Chang <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2021-chang-projection>`_ - Real-time multi-angle projection imaging of biological dynamics.
- `2022, Dean <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2021-dean-protocol>`_ - Isotropic imaging across spatial scales with axially swept light-sheet microscopy.
- `2022, Chang <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2022-chen>`_ - Resolution doubling in light-sheet microscopy via oblique plane structured illumination.
- `2023, Chang <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2023-POPSIM>`_ - Projective oblique plane structured illumination microscopy.
- `TBD, Isogai <https://github.com/AdvancedImagingUTSW/manuscripts/tree/main/2022-isogai>`_ - Direct Arp2/3-vinculin binding is essential for cell spreading, but only on compliant substrates and in 3D.