From bf26ae17c608d9e1873acd5bf54cf9f571ce5c52 Mon Sep 17 00:00:00 2001
From: Alex Gavryushkin <alex@biods.org>
Date: Thu, 14 Mar 2024 15:17:04 +0100
Subject: [PATCH] DKFZ slides -- getting there

---
 talks/2024_DKFZ_Alex.html | 105 ++++++++++++++++++++++++++++++++++----
 1 file changed, 95 insertions(+), 10 deletions(-)

diff --git a/talks/2024_DKFZ_Alex.html b/talks/2024_DKFZ_Alex.html
index 2331e18..1c252c5 100644
--- a/talks/2024_DKFZ_Alex.html
+++ b/talks/2024_DKFZ_Alex.html
@@ -52,36 +52,121 @@ <h4>Phylogenetic trees on tumor cells</h4>
 	<img data-src="./images/tumor_cell_tree.svg" width=80%>
 </section>
 
-<section data-background-image="./images/multiomic_cancer_evo.svg">
+<section data-background-image="./images/multiomic_cancer_evo.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/spatial_phylo_on_all_cells.svg">
+<section data-background-image="./images/spatial_phylo_on_all_cells.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/pathologist_annotated_cells.svg">
+<section data-background-image="./images/pathologist_annotated_cells.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/twenty_quality_cells.svg">
+<section data-background-image="./images/twenty_quality_cells.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/cells_with_same_genotypes.svg">
+<section data-background-image="./images/cells_with_same_genotypes.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/tree_on_all_quality_cells_expression.svg">
+<section data-background-image="./images/tree_on_all_quality_cells_expression.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/tree_on_cells_with_same_genotype_expression.svg">
+<section data-background-image="./images/tree_on_cells_with_same_genotype_expression.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/tree_on_cells_with_same_genotype_snv.svg">
+<section data-background-image="./images/tree_on_cells_with_same_genotype_snv.svg"
+	data-background-size=80%>
 </section>
 
-<section data-background-image="./images/tree_on_cells_with_same_genotype_expression_snv.svg">
+<section data-background-image="./images/tree_on_cells_with_same_genotype_expression_snv.svg"
+	data-background-size=80%>
 </section>
 
 <section>
 	<h3>Problem</h3>
-	<h4>This is not reproducible!</h4>
+	<h4>This result is not consistent across datasets &mdash; why?</h4>
+</section>
+
+<section data-background-image="./images/visium_patient_one.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_patient_two.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_challanges.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_challanges_we_tackle.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/expression_data_discretization.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/gene_filtering_options.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/patient_two_maxlik.svg"
+	data-background-size=50%>
+</section>
+
+<section data-background-image="./images/patient_one_maxlik.svg"
+	data-background-size=50%>
+</section>
+
+<section data-background-image="./images/visium_pathologist_annotation_both_patients.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p1_tumor2_test.svg"
+	data-background-size=60%>
+</section>
+
+<section data-background-image="./images/visium_expected_clades.svg"
+	data-background-size=60%>
+</section>
+
+<section data-background-image="./images/visium_manually_selected_cells.svg"
+	data-background-size=60%>
+</section>
+
+<section data-background-image="./images/visium_patien1_bayesian_tree.svg"
+	data-background-size=60%>
+</section>
+
+<section data-background-image="./images/visium_p1_highest_counts.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p1_highest_counts_bayesian_tree.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p1_similar_counts.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p1_similar_counts_bayesian_tree.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p2_similar_counts.svg"
+	data-background-size=70%>
+</section>
+
+<section data-background-image="./images/visium_p2_similar_counts_bayesian_tree.svg"
+	data-background-size=70%>
 </section>
 
 <section>