pearsonlab · jmxpearson · May 12, 2026 · May 12, 2026 · May 12, 2026 · May 12, 2026
diff --git a/_data/research.yml b/_data/research.yml
@@ -28,7 +28,7 @@
     Together with [Eva Naumann's](https://www.neuro.duke.edu/research/faculty-labs/naumann-lab) lab, we've developed *[improv](https://github.com/project-improv/improv)* ([paper](https://www.biorxiv.org/content/10.1101/2021.02.22.432006v1)), a software platform for designing and orchestrating adaptive experiments. By analyzing data in real time, we can measure, model, and manipulate neural activity in response to new data. We've shown how these tools, in conjunction with holographic photostimulation, could in principle map functional connectivity of large circuits in a few hours ([paper](https://proceedings.nips.cc/paper/2020/file/531d29a813ef9471aad0a5558d449a73-Paper.pdf), [expanded version](https://arxiv.org/abs/2007.13911)). More recently, we've worked on methods for fast dimensionality reduction and modeling of neural populations in real time ([paper](https://arxiv.org/abs/2108.13941)).
 
     <figure>
-      <img src="/images/pipelineNewpng3.png" class="img-responsive" alt="Closed-loop pipeline concept">
+      <img src="/images/pipelineNewpng3.png" class="img-fluid" alt="Closed-loop pipeline concept">
       <figcaption>
         Concept for the closed-loop pipeline. Neural data from the zebrafish are collected in the form of images, preprocessed, and analyzed in real-time. Targets for optical stimulation are then chosen based on the results of this analysis, creating adaptive experiments that test causal hypotheses.
       </figcaption>

diff --git a/_includes/blog_image.html b/_includes/blog_image.html
@@ -1,4 +1,4 @@
 <table class="image">
 <caption style="caption-side: bottom; font-size: 0.75em">{{ include.description }}</caption>
-<tr><td><img class="img-responsive" src="{{ include.url }}" alt="{{ include.description }}" style="width: 50%"></td></tr>
+<tr><td><img class="img-fluid" src="{{ include.url }}" alt="{{ include.description }}" style="width: 50%"></td></tr>
 </table>
diff --git a/_includes/head.html b/_includes/head.html
@@ -21,14 +21,13 @@
     <link rel="icon" type="image/png" sizes="16x16" href="/images/icons/favicon-16x16.png">
     <meta name="theme-color" content="#ffffff">
 
-    <!-- Bootstrap core CSS from MaxCDN-->
-    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css" integrity="sha512-dTfge/zgoMYpP7QbHy4gWMEGsbsdZeCXz7irItjcC3sPUFtf0kuFbDz/ixG7ArTxmDjLXDmezHubeNikyKGVyQ==" crossorigin="anonymous">
+    <!-- Bootstrap 5 core CSS -->
+    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH" crossorigin="anonymous">
 
     <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css">
 
     <!-- Custom styles for this template -->
     <link href="/css/custom.css" rel="stylesheet">
-    <link href="/css/bootstrap-social.css" rel="stylesheet">
 
     {% if page.extra_head %}{{ page.extra_head }}{% endif %}
 </head>
diff --git a/_includes/jsload.html b/_includes/jsload.html
@@ -1,11 +1,6 @@
-<!-- Bootstrap core JavaScript
-================================================== -->
-<!-- Placed at the end of the document so the pages load faster -->
-<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
-<script src="//netdna.bootstrapcdn.com/bootstrap/3.0.0/js/bootstrap.min.js"></script>
+<!-- JavaScript at end of body for fast first paint.
+     Bootstrap 5 is jQuery-free; bundle includes Popper for tooltips. -->
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz" crossorigin="anonymous"></script>
 <script type="text/javascript" async
     src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
 </script>
-<script src="/js/jumbo_scroll.js"></script>
-<!-- IE10 viewport hack for Surface/desktop Windows 8 bug -->
-<script src="https://maxcdn.bootstrapcdn.com/js/ie10-viewport-bug-workaround.js"></script>
diff --git a/_includes/jumbotron.html b/_includes/jumbotron.html
@@ -1,4 +1,3 @@
-<div class="bg"></div>
 <div class="jumbotron">
   <div class="container">
     <br>

diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -1,29 +1,23 @@
-<nav class="navbar navbar-inverse navbar-fixed-top">
+<nav class="navbar navbar-expand-md navbar-dark bg-dark fixed-top">
   <div class="container-fluid">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
-        <span class="sr-only">Toggle navigation</span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <a class="navbar-brand" href='/'><b>[ &lambda; ]</b></a>
-    </div>
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
+    <a class="navbar-brand" href="/"><b>[ &lambda; ]</b></a>
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+    <div class="collapse navbar-collapse" id="navbar">
+      <ul class="navbar-nav">
         <!-- Generate navbar based on 'nav' variable in page headers -->
         {% for other in site.pages %}
           {% if other.nav %}
             {% if other.title == page.title %}
-              <li class="active"><a href={{ other.url }}>{{other.nav}} <span class="sr-only">(current)</span></a></li>
+              <li class="nav-item"><a class="nav-link active" aria-current="page" href="{{ other.url }}">{{ other.nav }}</a></li>
             {% else %}
-              <li><a href={{ other.url }}>{{other.nav}}</a></li>
+              <li class="nav-item"><a class="nav-link" href="{{ other.url }}">{{ other.nav }}</a></li>
             {% endif %}
           {% endif %}
         {% endfor %}
-        <!-- <li><a href="https://github.com/pearsonlab">Code</a></li> -->
-        <li><a href="https://github.com/pearsonlab/pearsonlab.github.io/wiki">Wiki</a></li>
+        <li class="nav-item"><a class="nav-link" href="https://github.com/pearsonlab/pearsonlab.github.io/wiki">Wiki</a></li>
       </ul>
-    </div><!--/.navbar-collapse -->
+    </div>
   </div>
 </nav>
diff --git a/_includes/person.html b/_includes/person.html
@@ -1,6 +1,6 @@
 {% assign person = include.person %}
 <div class="col-md-6 person-card">
-  <img class="img-circle person-photo" src="{{ person.image }}" alt="{{ person.name }}">
+  <img class="rounded-circle person-photo" src="{{ person.image }}" alt="{{ person.name }}">
   <h2>{{ person.name }}</h2>
   {% if person.title %}<p class="person-title"><em>{{ person.title }}</em></p>{% endif %}
   <p class="person-desc">
@@ -9,37 +9,37 @@ <h2>{{ person.name }}</h2>
   <!-- Social Icons -->
   <p class="person-social">
     {% if person.site %}
-    <a class="btn btn-social-icon btn-microsoft" href="{{ person.site }}" aria-label="Personal site">
+    <a class="social-icon social-icon-site" href="{{ person.site }}" aria-label="Personal site">
       <i class="fa fa-globe"></i>
     </a>
     {% endif %}
     {% if person.github %}
-    <a class="btn btn-social-icon btn-github" href="{{ person.github }}" aria-label="GitHub">
+    <a class="social-icon social-icon-github" href="{{ person.github }}" aria-label="GitHub">
       <i class="fa fa-github"></i>
     </a>
     {% endif %}
     {% if person.email %}
-    <a class="btn btn-social-icon btn-google" href="mailto:{{ person.email }}" aria-label="Email">
+    <a class="social-icon social-icon-email" href="mailto:{{ person.email }}" aria-label="Email">
       <i class="fa fa-envelope"></i>
     </a>
     {% endif %}
     {% if person.linkedin %}
-    <a class="btn btn-social-icon btn-linkedin" href="{{ person.linkedin }}" aria-label="LinkedIn">
+    <a class="social-icon social-icon-linkedin" href="{{ person.linkedin }}" aria-label="LinkedIn">
       <i class="fa fa-linkedin"></i>
     </a>
     {% endif %}
     {% if person.scholar %}
-    <a class="person-svg-icon person-icon-scholar" href="{{ person.scholar }}" aria-label="Google Scholar">
+    <a class="social-icon social-icon-scholar" href="{{ person.scholar }}" aria-label="Google Scholar">
       <svg viewBox="0 0 24 24" fill="currentColor" aria-hidden="true"><path d="M5.242 13.769L0 9.5 12 0l12 9.5-5.242 4.269C17.548 11.249 14.978 9.5 12 9.5c-2.977 0-5.548 1.748-6.758 4.269zM12 10a7 7 0 1 0 0 14 7 7 0 0 0 0-14z"/></svg>
     </a>
     {% endif %}
     {% if person.bluesky %}
-    <a class="person-svg-icon person-icon-bluesky" href="{{ person.bluesky }}" aria-label="Bluesky">
+    <a class="social-icon social-icon-bluesky" href="{{ person.bluesky }}" aria-label="Bluesky">
       <svg viewBox="0 0 24 24" fill="currentColor" aria-hidden="true"><path d="M5.202 2.857C7.954 4.922 10.913 9.11 12 11.358c1.087-2.247 4.046-6.436 6.798-8.501C20.783 1.366 24 .213 24 3.883c0 .732-.42 6.156-.667 7.037-.856 3.061-3.978 3.842-6.755 3.37 4.854.826 6.089 3.562 3.422 6.299-5.065 5.196-7.28-1.304-7.847-2.97-.104-.305-.152-.448-.153-.327 0-.121-.05.022-.153.327-.568 1.666-2.782 8.166-7.847 2.97-2.667-2.737-1.432-5.473 3.422-6.3-2.777.473-5.899-.308-6.755-3.369C.42 10.04 0 4.615 0 3.883c0-3.67 3.217-2.517 5.202-1.026"/></svg>
     </a>
     {% endif %}
     {% if person.orcid %}
-    <a class="person-svg-icon person-icon-orcid" href="{{ person.orcid }}" aria-label="ORCID">
+    <a class="social-icon social-icon-orcid" href="{{ person.orcid }}" aria-label="ORCID">
       <svg viewBox="0 0 24 24" fill="currentColor" aria-hidden="true"><path d="M12 0C5.372 0 0 5.372 0 12s5.372 12 12 12 12-5.372 12-12S18.628 0 12 0zM7.369 4.378c.525 0 .947.431.947.947s-.422.947-.947.947a.95.95 0 0 1-.947-.947c0-.525.422-.947.947-.947zm-.722 3.038h1.444v10.041H6.647V7.416zm3.562 0h3.9c3.712 0 5.344 2.653 5.344 5.025 0 2.578-2.016 5.025-5.325 5.025h-3.919V7.416zm1.444 1.303v7.444h2.297c3.272 0 4.022-2.484 4.022-3.722 0-2.016-1.284-3.722-4.097-3.722h-2.222z"/></svg>
     </a>
     {% endif %}

diff --git a/_posts/2015-11-06-announcing_plab.md b/_posts/2015-11-06-announcing_plab.md
@@ -6,7 +6,7 @@ author: John Pearson
 category: blog
 ---
 
-<img class="img-responsive" src="/images/plab_logotype.svg" alt="Pearson Lab logotype" style="width: 40%">
+<img class="img-fluid" src="/images/plab_logotype.svg" alt="Pearson Lab logotype" style="width: 40%">
 
 Today, we're launching the website for P[&lambda;]ab, the Pearson Lab at Duke University. The plan is to use this blog for lab news, ongoing projects, and things we just think are cool.
 

diff --git a/_posts/2015-11-13-big-data-nih.md b/_posts/2015-11-13-big-data-nih.md
@@ -6,7 +6,7 @@ author: John Pearson
 category: blog
 ---
 
-<img class="img-responsive" src="http://people.duke.edu/~jmp33/assets/bd2k.png" alt="NIH Big Data to Knowledge (BD2K) banner" style="width: 90%">
+<img class="img-fluid" src="http://people.duke.edu/~jmp33/assets/bd2k.png" alt="NIH Big Data to Knowledge (BD2K) banner" style="width: 90%">
 
 > Big data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it...
 >