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diff --git a/2024_05_20/.DS_Store b/2024_05_20/.DS_Store
diff --git a/2024_05_20/.buildinfo b/2024_05_20/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 3626d7b82b997f0e47c732dda567990c
+config: d20766c83d1ea9a575acfd08d22d6836
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/2024_05_20/.doctrees/01_intro_image_analysis.doctree b/2024_05_20/.doctrees/01_intro_image_analysis.doctree
diff --git a/2024_05_20/.doctrees/02_intro_qupath.doctree b/2024_05_20/.doctrees/02_intro_qupath.doctree
diff --git a/2024_05_20/.doctrees/03_qupath_projects_and_GUI.doctree b/2024_05_20/.doctrees/03_qupath_projects_and_GUI.doctree
diff --git a/2024_05_20/.doctrees/04_cell_detection.doctree b/2024_05_20/.doctrees/04_cell_detection.doctree
diff --git a/2024_05_20/.doctrees/05_cell_classification.doctree b/2024_05_20/.doctrees/05_cell_classification.doctree
diff --git a/2024_05_20/.doctrees/06_tissue_annotation.doctree b/2024_05_20/.doctrees/06_tissue_annotation.doctree
diff --git a/2024_05_20/.doctrees/07_scripting_workflows.doctree b/2024_05_20/.doctrees/07_scripting_workflows.doctree
diff --git a/2024_05_20/.doctrees/environment.pickle b/2024_05_20/.doctrees/environment.pickle
diff --git a/2024_05_20/.doctrees/index.doctree b/2024_05_20/.doctrees/index.doctree
diff --git a/2024_05_20/01_intro_image_analysis.html b/2024_05_20/01_intro_image_analysis.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="introduction-to-image-analysis">
 <h1>Introduction to image analysis<a class="headerlink" href="#introduction-to-image-analysis" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/02_intro_qupath.html b/2024_05_20/02_intro_qupath.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="introduction-to-qupath">
 <h1>Introduction to QuPath<a class="headerlink" href="#introduction-to-qupath" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/03_qupath_projects_and_GUI.html b/2024_05_20/03_qupath_projects_and_GUI.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="qupath-projects-and-user-interface">
 <h1>QuPath projects and user-interface<a class="headerlink" href="#qupath-projects-and-user-interface" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/04_cell_detection.html b/2024_05_20/04_cell_detection.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="cell-detection-and-measurements">
 <h1>Cell detection and measurements<a class="headerlink" href="#cell-detection-and-measurements" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/05_cell_classification.html b/2024_05_20/05_cell_classification.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="cell-classification">
 <h1>Cell classification<a class="headerlink" href="#cell-classification" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/05_cell_classification.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/05_cell_classification.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/06_tissue_annotation.html b/2024_05_20/06_tissue_annotation.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="tissue-annotation-and-spatial-measurements">
 <h1>Tissue annotation and spatial measurements<a class="headerlink" href="#tissue-annotation-and-spatial-measurements" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/07_scripting_workflows.html b/2024_05_20/07_scripting_workflows.html
@@ -425,7 +425,7 @@ <h3>Versions</h3>
 
   <section id="scripting-workflows-and-batch-processing">
 <h1>Scripting, workflows and batch processing<a class="headerlink" href="#scripting-workflows-and-batch-processing" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_05_20/_sources/01_intro_image_analysis.rst.txt b/2024_05_20/_sources/01_intro_image_analysis.rst.txt
@@ -3,4 +3,4 @@ Introduction to image analysis
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe>
diff --git a/2024_05_20/_sources/02_intro_qupath.rst.txt b/2024_05_20/_sources/02_intro_qupath.rst.txt
@@ -3,5 +3,5 @@ Introduction to QuPath
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/03_qupath_projects_and_GUI.rst.txt b/2024_05_20/_sources/03_qupath_projects_and_GUI.rst.txt
@@ -3,5 +3,5 @@ QuPath projects and user-interface
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/04_cell_detection.rst.txt b/2024_05_20/_sources/04_cell_detection.rst.txt
@@ -3,5 +3,5 @@ Cell detection and measurements
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/05_cell_classification.rst.txt b/2024_05_20/_sources/05_cell_classification.rst.txt
@@ -3,5 +3,5 @@ Cell classification
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/05_cell_classification.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/05_cell_classification.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/06_tissue_annotation.rst.txt b/2024_05_20/_sources/06_tissue_annotation.rst.txt
@@ -3,5 +3,5 @@ Tissue annotation and spatial measurements
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/07_scripting_workflows.rst.txt b/2024_05_20/_sources/07_scripting_workflows.rst.txt
@@ -3,5 +3,5 @@ Scripting, workflows and batch processing
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_05_20/_sources/index.rst.txt b/2024_05_20/_sources/index.rst.txt
@@ -17,7 +17,7 @@ These materials were initially designed for a workshop taught in-person at Harva
 
 .. raw:: html
 
-   <p>1. Slides: <a href="docs/source/_static/all_slides.pdf" download>Download PDF</a></p>
+   <p>1. Slides: <a href="_static/all_slides.pdf" download>Download PDF</a></p>
 
 Contents
 =======================================

diff --git a/2024_05_20/index.html b/2024_05_20/index.html
@@ -399,7 +399,7 @@ <h1>Introduction to Bioimage Analysis using QuPath<a class="headerlink" href="#i
 It is designed as a primer on QuPath for busy biologists who need to analyze images part of their research.</p>
 <p>These materials were initially designed for a workshop taught in-person at Harvard Medical School - organized by the <a class="reference external" href="https://iac.hms.harvard.edu/">Image Analysis Collaboratory</a>.</p>
 <p><strong>Download the course materials:</strong></p>
-<p>1. Slides: <a href="docs/source/_static/all_slides.pdf" download>Download PDF</a></p></section>
+<p>1. Slides: <a href="_static/all_slides.pdf" download>Download PDF</a></p></section>
 <section id="contents">
 <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">#</a></h1>
 <div class="toctree-wrapper compound">

diff --git a/2024_09_16/.buildinfo b/2024_09_16/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6ebc5f31a9b32ca52d6d1cbf2fa801e1
+config: 55d922c53fc0adb2ab38993bb0dec5fa
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/2024_09_16/.doctrees/01_intro_image_analysis.doctree b/2024_09_16/.doctrees/01_intro_image_analysis.doctree
diff --git a/2024_09_16/.doctrees/02_intro_qupath.doctree b/2024_09_16/.doctrees/02_intro_qupath.doctree
diff --git a/2024_09_16/.doctrees/03_qupath_projects_and_GUI.doctree b/2024_09_16/.doctrees/03_qupath_projects_and_GUI.doctree
diff --git a/2024_09_16/.doctrees/04_cell_detection.doctree b/2024_09_16/.doctrees/04_cell_detection.doctree
diff --git a/2024_09_16/.doctrees/05_cell_classification.doctree b/2024_09_16/.doctrees/05_cell_classification.doctree
diff --git a/2024_09_16/.doctrees/06_tissue_annotation.doctree b/2024_09_16/.doctrees/06_tissue_annotation.doctree
diff --git a/2024_09_16/.doctrees/07_scripting_workflows.doctree b/2024_09_16/.doctrees/07_scripting_workflows.doctree
diff --git a/2024_09_16/.doctrees/environment.pickle b/2024_09_16/.doctrees/environment.pickle
diff --git a/2024_09_16/.doctrees/index.doctree b/2024_09_16/.doctrees/index.doctree
diff --git a/2024_09_16/01_intro_image_analysis.html b/2024_09_16/01_intro_image_analysis.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="introduction-to-image-analysis">
 <h1>Introduction to image analysis<a class="headerlink" href="#introduction-to-image-analysis" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/02_intro_qupath.html b/2024_09_16/02_intro_qupath.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="introduction-to-qupath">
 <h1>Introduction to QuPath<a class="headerlink" href="#introduction-to-qupath" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/03_qupath_projects_and_GUI.html b/2024_09_16/03_qupath_projects_and_GUI.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="qupath-projects-and-user-interface">
 <h1>QuPath projects and user-interface<a class="headerlink" href="#qupath-projects-and-user-interface" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/04_cell_detection.html b/2024_09_16/04_cell_detection.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="cell-detection-and-measurements">
 <h1>Cell detection and measurements<a class="headerlink" href="#cell-detection-and-measurements" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/05_cell_classification.html b/2024_09_16/05_cell_classification.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="cell-classification">
 <h1>Cell classification<a class="headerlink" href="#cell-classification" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/05_cell_classification.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/05_cell_classification.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/06_tissue_annotation.html b/2024_09_16/06_tissue_annotation.html
@@ -426,7 +426,7 @@ <h3>Versions</h3>
 
   <section id="tissue-annotation-and-spatial-measurements">
 <h1>Tissue annotation and spatial measurements<a class="headerlink" href="#tissue-annotation-and-spatial-measurements" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/07_scripting_workflows.html b/2024_09_16/07_scripting_workflows.html
@@ -425,7 +425,7 @@ <h3>Versions</h3>
 
   <section id="scripting-workflows-and-batch-processing">
 <h1>Scripting, workflows and batch processing<a class="headerlink" href="#scripting-workflows-and-batch-processing" title="Link to this heading">#</a></h1>
-<iframe src="docs/source/_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe></section>
+<iframe src="_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe></section>
 
 
                 </article>

diff --git a/2024_09_16/_sources/01_intro_image_analysis.rst.txt b/2024_09_16/_sources/01_intro_image_analysis.rst.txt
@@ -3,4 +3,4 @@ Introduction to image analysis
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/01_intro_digital_image_analysis.pdf" width="100%" height="600px"></iframe>
diff --git a/2024_09_16/_sources/02_intro_qupath.rst.txt b/2024_09_16/_sources/02_intro_qupath.rst.txt
@@ -3,5 +3,5 @@ Introduction to QuPath
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/02_intro_qupath.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/03_qupath_projects_and_GUI.rst.txt b/2024_09_16/_sources/03_qupath_projects_and_GUI.rst.txt
@@ -3,5 +3,5 @@ QuPath projects and user-interface
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/03_qupath_projects_and_GUI.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/04_cell_detection.rst.txt b/2024_09_16/_sources/04_cell_detection.rst.txt
@@ -3,5 +3,5 @@ Cell detection and measurements
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/04_cell_detection_and_measurements.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/05_cell_classification.rst.txt b/2024_09_16/_sources/05_cell_classification.rst.txt
@@ -3,5 +3,5 @@ Cell classification
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/05_cell_classification.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/05_cell_classification.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/06_tissue_annotation.rst.txt b/2024_09_16/_sources/06_tissue_annotation.rst.txt
@@ -3,5 +3,5 @@ Tissue annotation and spatial measurements
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/06_tissue_annotation_and_spatial.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/07_scripting_workflows.rst.txt b/2024_09_16/_sources/07_scripting_workflows.rst.txt
@@ -3,5 +3,5 @@ Scripting, workflows and batch processing
 
 .. raw:: html
 
-   <iframe src="docs/source/_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe>
+   <iframe src="_static/07_scripting_workflow_and_batch_processing.pdf" width="100%" height="600px"></iframe>
 
diff --git a/2024_09_16/_sources/index.rst.txt b/2024_09_16/_sources/index.rst.txt
@@ -17,7 +17,7 @@ These materials were initially designed for a workshop taught in-person at Harva
 
 .. raw:: html
 
-   <p>1. Slides: <a href="docs/source/_static/all_slides.pdf" download>Download PDF</a></p>
+   <p>1. Slides: <a href="_static/all_slides.pdf" download>Download PDF</a></p>
 
 Contents
 =======================================

diff --git a/2024_09_16/index.html b/2024_09_16/index.html
@@ -399,7 +399,7 @@ <h1>Introduction to Bioimage Analysis using QuPath<a class="headerlink" href="#i
 It is designed as a primer on QuPath for busy biologists who need to analyze images part of their research.</p>
 <p>These materials were initially designed for a workshop taught in-person at Harvard Medical School - organized by the <a class="reference external" href="https://iac.hms.harvard.edu/">Image Analysis Collaboratory</a>.</p>
 <p><strong>Download the course materials:</strong></p>
-<p>1. Slides: <a href="docs/source/_static/all_slides.pdf" download>Download PDF</a></p></section>
+<p>1. Slides: <a href="_static/all_slides.pdf" download>Download PDF</a></p></section>
 <section id="contents">
 <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">#</a></h1>
 <div class="toctree-wrapper compound">