Small update

Author: AdvancedImagingUTSW

.gitignore

@@ -1,19 +1,6 @@
 
 .idea/*
 .ds_store
-!Build/
-
-#/.build/
-#
-## Module::Build
-#build/
-#build/html/*
-#build
-#Build.bat
-#
-#```
-#build/html/*
-#*.doctree
-#*.js
-#*.html
-#build/doctrees/_templates/custom_module.doctree
+build/*
+/build/
+*.html

source/2024-01-09-LungExpansion2.png

@@ -1,50 +1,15 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-#sys.path.insert(0, os.path.abspath("../../src"))
-
+import datetime
 
 # -- Project information -----------------------------------------------------
-
+year = datetime.date.today().year
 project = "The Dean Lab"
-copyright = "2023, Dean Lab, UT Southwestern Medical Center"
+copyright = f"{year}, Dean Lab, UT Southwestern Medical Center"
 author = "Dean Lab, UT Southwestern Medical Center"
 
 
 # -- General configuration ---------------------------------------------------
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-# extensions = [
-#     "sphinx.ext.duration",
-#     "sphinx.ext.doctest",
-#     "sphinx.ext.autodoc",
-#     "sphinx.ext.autosummary",
-#     "sphinx.ext.githubpages",
-#     "sphinx.ext.napoleon",
-#     "sphinx.ext.coverage",
-#     "sphinx_toolbox.collapse",
-#     "sphinx.ext.autosectionlabel",
-# ]
-
 autosectionlabel_prefix_document = True
-
-# Boolean indicating whether to scan all found documents for
-# autosummary directives, and to generate stub pages for each
-# (http://sphinx-doc.org/latest/ext/autosummary.html)
 autosummary_generate = False
 
 # Both the class’ and the __init__ method’s docstring are concatenated
@@ -70,9 +35,6 @@
 
 autodoc_inherit_docstrings = True
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["./_templates"]
-
 # The suffix of source filenames.
 source_suffix = ".rst"
 
@@ -102,6 +64,6 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 # html_static_path = ["_static"]
 
-html_logo = "dean_lab.png"
+html_logo = "cell.png"
 
 pygments_style = "sphinx"

source/_templates/custom_class.rst

@@ -1,15 +1,9 @@
 
 .. _dean-lab-home:
 
-######################################################
+####################
 The Dean Lab at UTSW
-######################################################
-
-
-.. image:: 2024-01-09-LungExpansion2.png
-    :width: 100%
-    :alt: An expanded mouse lung imaged with Axially Swept Light-Sheet Microscopy
-    :align: center
+####################
 
 The Dean Lab is a multi-disciplinary team of biologists, chemists, physicists, and engineers
 at the University of Texas Southwestern Medical Center in Dallas, Texas. We develop
@@ -18,40 +12,36 @@ complex tissue contexts. Our goal is to understand how cells make decisions in t
 of their native environment, and how these decisions go awry in disease. More information
 about our research can be found on our `website <https://www.dean-lab.org>`_.
 
-**Projects**
-=============
+---------------
+
+**Research Projects**
+=====================
 
-- Light-sheet microscopy software packages for intelligent imaging of complex tissue samples
+- `navigate <https://thedeanlab.github.io/navigate/>`_ - Light-sheet microscopy software packages for intelligent imaging of complex tissue samples. navigate is equipped with a series of plugins that extend its functionality, enabling the use of `robotics <https://github.com/TheDeanLab/navigate-at-scale>`_, imaging cells in a `projection format <https://github.com/TheDeanLab/navigate-confocal-projection>`_, accessing additional `hardware <https://github.com/TheDeanLab/navigate-mmcore-plugin>`_, and leveraging real-time feedback from `ilastik  <https://github.com/TheDeanLab/navigate-ilastik-server>`_. To enable users to generate their own plugins, we provide a `plugin template <https://github.com/TheDeanLab/navigate-plugin-template>`_.
 
-- Tissue clearing and labeling protocols for high-resolution imaging deep within
-  biological specimens.
+- `Altair <https://thedeanlab.github.io/altair/>`_ - A series of cost-effective, easy-to-assemble, and performant light-sheet microscopes for interrogating cells and tissues at the highest resolution.
+
+---------------
 
-- Cost-effective, easy-to-assemble, and performant light-sheet microscopes for interrogating live cells,
-  expanded, and cleared tissue samples.
 
 **Educational Resources**
-================
+=========================
+
 - `CI2023 <https://github.com/TheDeanLab/CI2023>`_ - An introduction to continuous integration and continuous deployment for scientific software.
 
+---------------
+
 **Publication Repositories**
-================
+============================
+
 For many manuscripts published over the years, we provide access to CAD files, software, and data
-via GitHub. These repositories are organized by publication year.
-
-- `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.
-
-**Funding**
-============
+via GitHub. These repositories are organized by publication year. You can find this information :ref:`publications-home`.
+
+---------------
+
+
+**Our Supporters**
+==================
 
 The **Dean Lab** is supported by the following funding sources:
 
@@ -61,12 +51,9 @@ The **Dean Lab** is supported by the following funding sources:
 - `UTSW President's Research Council <https://engage.utsouthwestern.edu/pages/membership-giving/membership-giving---presidents-research-council>`_
 
 .. toctree::
-   :caption: Software
+   :caption: Repositories
    :maxdepth: 2
 
-   navigate <https://github.com/TheDeanLab/navigate>
-   navigate Plugin Template <https://github.com/TheDeanLab/navigate-plugin-template>
-   navigate Confocal Projection Plugin <https://github.com/TheDeanLab/navigate-confocal-projection>
-   navigate At Scale <https://github.com/TheDeanLab/navigate-at-scale>
-   navigate MMCore Plugin <https://github.com/TheDeanLab/navigate-mmcore-plugin>
-   navigate ilastik Server <https://github.com/TheDeanLab/navigate-ilastik-server>
+   navigate <https://thedeanlab.github.io/navigate/>
+   altair <https://thedeanlab.github.io/altair/>
+

source/_templates/custom_module.rst

@@ -0,0 +1,21 @@
+
+.. _publications-home:
+
+########################
+Publication Repositories
+########################
+
+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.