diff --git a/pyrovelocity/config.py b/pyrovelocity/config.py
index 5eaf54ff7..b1e55ac55 100644
--- a/pyrovelocity/config.py
+++ b/pyrovelocity/config.py
@@ -525,6 +525,7 @@ def create_reports_config(model_name: str, model_number: int):
             uncertainty_param_plot=f"{path}/param_uncertainties.pdf",
             vector_field_plot=f"{path}/vector_field.pdf",
             posterior_phase_portraits=f"{path}/posterior_phase_portraits",
+            t0_selection=f"{path}/t0_selection.tif",
             biomarker_selection_plot=f"{path}/markers_selection_scatterplot.tif",
             biomarker_phaseportrait_plot=f"{path}/markers_phaseportrait.pdf",
             fig2_part1_plot=f"{path}/fig2_part1_plot.pdf",
diff --git a/reproducibility/figures/config.yaml b/reproducibility/figures/config.yaml
index c74c8e416..40d4b89b7 100644
--- a/reproducibility/figures/config.yaml
+++ b/reproducibility/figures/config.yaml
@@ -699,6 +699,7 @@ reports:
       uncertainty_param_plot: reports/pancreas_model2/param_uncertainties.pdf
       vector_field_plot: reports/pancreas_model2/vector_field.pdf
       posterior_phase_portraits: reports/pancreas_model2/posterior_phase_portraits
+      t0_selection: reports/pancreas_model2/t0_selection.tif
       biomarker_selection_plot: reports/pancreas_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pancreas_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pancreas_model2/fig2_part1_plot.pdf
@@ -716,6 +717,7 @@ reports:
       uncertainty_param_plot: reports/bonemarrow_model2/param_uncertainties.pdf
       vector_field_plot: reports/bonemarrow_model2/vector_field.pdf
       posterior_phase_portraits: reports/bonemarrow_model2/posterior_phase_portraits
+      t0_selection: reports/bonemarrow_model2/t0_selection.tif
       biomarker_selection_plot: reports/bonemarrow_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/bonemarrow_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/bonemarrow_model2/fig2_part1_plot.pdf
@@ -733,6 +735,7 @@ reports:
       uncertainty_param_plot: reports/pbmc68k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc68k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc68k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc68k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc68k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc68k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc68k_model2/fig2_part1_plot.pdf
@@ -750,6 +753,7 @@ reports:
       uncertainty_param_plot: reports/pons_model2/param_uncertainties.pdf
       vector_field_plot: reports/pons_model2/vector_field.pdf
       posterior_phase_portraits: reports/pons_model2/posterior_phase_portraits
+      t0_selection: reports/pons_model2/t0_selection.tif
       biomarker_selection_plot: reports/pons_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pons_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pons_model2/fig2_part1_plot.pdf
@@ -767,6 +771,7 @@ reports:
       uncertainty_param_plot: reports/pbmc10k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc10k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc10k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc10k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc10k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc10k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc10k_model2/fig2_part1_plot.pdf
@@ -784,6 +789,7 @@ reports:
       uncertainty_param_plot: reports/pbmc5k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc5k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc5k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc5k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc5k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc5k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc5k_model2/fig2_part1_plot.pdf
@@ -801,6 +807,7 @@ reports:
       uncertainty_param_plot: reports/larry_tips_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_tips_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_tips_model2/posterior_phase_portraits
+      t0_selection: reports/larry_tips_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_tips_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_tips_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_tips_model2/fig2_part1_plot.pdf
@@ -818,6 +825,7 @@ reports:
       uncertainty_param_plot: reports/larry_mono_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_mono_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_mono_model2/posterior_phase_portraits
+      t0_selection: reports/larry_mono_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_mono_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_mono_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_mono_model2/fig2_part1_plot.pdf
@@ -835,6 +843,7 @@ reports:
       uncertainty_param_plot: reports/larry_neu_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_neu_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_neu_model2/posterior_phase_portraits
+      t0_selection: reports/larry_neu_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_neu_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_neu_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_neu_model2/fig2_part1_plot.pdf
@@ -852,6 +861,7 @@ reports:
       uncertainty_param_plot: reports/larry_multilineage_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_multilineage_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_multilineage_model2/posterior_phase_portraits
+      t0_selection: reports/larry_multilineage_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_multilineage_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_multilineage_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_multilineage_model2/fig2_part1_plot.pdf
@@ -869,6 +879,7 @@ reports:
       uncertainty_param_plot: reports/larry_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_model2/posterior_phase_portraits
+      t0_selection: reports/larry_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_model2/fig2_part1_plot.pdf
diff --git a/reproducibility/figures/dvc.lock b/reproducibility/figures/dvc.lock
index 3e30f9aab..a564e0c5c 100644
--- a/reproducibility/figures/dvc.lock
+++ b/reproducibility/figures/dvc.lock
@@ -1952,8 +1952,8 @@ stages:
       md5: 5488e83a70c427afd51f264f35e72735
       size: 492128112
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -1971,6 +1971,7 @@ stages:
           uncertainty_param_plot: reports/pancreas_model2/param_uncertainties.pdf
           vector_field_plot: reports/pancreas_model2/vector_field.pdf
           posterior_phase_portraits: reports/pancreas_model2/posterior_phase_portraits
+          t0_selection: reports/pancreas_model2/t0_selection.tif
           biomarker_selection_plot: reports/pancreas_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/pancreas_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/pancreas_model2/fig2_part1_plot.pdf
@@ -1982,52 +1983,52 @@ stages:
       md5: bbff19677beed1c7cf3766506f391723
       size: 12359084
     - path: reports/pancreas_model2/clusters_violin_lin.pdf
-      md5: 17d957868b7deaee6d8288528db0431e
+      md5: 271c3d0798994c7eebe50b6f78f253b9
       size: 127497
     - path: reports/pancreas_model2/clusters_violin_lin.pdf.png
       md5: e30d28abc83a29951318f37d7a312ab4
       size: 2356560
     - path: reports/pancreas_model2/clusters_violin_log.pdf
-      md5: ee582c99e2a751dfa1cd71ab9b8e233c
+      md5: 15905d7d81802e85ad94f44c06fde0c8
       size: 128507
     - path: reports/pancreas_model2/clusters_violin_log.pdf.png
       md5: d7bd94742d8cbd0b1c7d56476a47512f
       size: 2452889
     - path: reports/pancreas_model2/fig2_part1_plot.pdf
-      md5: 6fbba4f9d5cac905b9772d8528f5c1bb
+      md5: 7d1d883b1065190d1cade4c2f9d2e820
       size: 431713
     - path: reports/pancreas_model2/fig2_part1_plot.pdf.png
       md5: 8ef3e40c15766142c8de633bda62c254
       size: 630588
     - path: reports/pancreas_model2/fig2_part2_plot.pdf
-      md5: ac5d0fa55c4313ece8aabebfb4c0d473
+      md5: 611d81a9a51761b012aa34182f78490b
       size: 1279288
     - path: reports/pancreas_model2/fig2_part2_plot.pdf.png
       md5: c2d29693ba60530c975f2115e9f495b5
       size: 685709
     - path: reports/pancreas_model2/param_uncertainties.pdf
-      md5: 24aa7f052ed96eb205a5a5c6b0e4f673
+      md5: 6ec0170659f17ef5f02d2b80c9558aff
       size: 140075
     - path: reports/pancreas_model2/param_uncertainties.pdf.png
       md5: 3f88d6dc17bda0f42c8f436e7382f454
       size: 782898
     - path: reports/pancreas_model2/rainbow.pdf
-      md5: 2d2b2069f346dfab9d6738a2236c3bdc
+      md5: 347bcddd19aa6ea9ea9f66187393ec65
       size: 5213471
     - path: reports/pancreas_model2/rainbow.pdf.png
       md5: 4df1b65124602086846e1b799b0b0fb4
       size: 1374852
     - path: reports/pancreas_model2/shared_time.pdf
-      md5: 98d27c1073895af5515a9d1597e983ff
+      md5: 6d25d34ccd5bf192b3ad81fb894f315c
       size: 284036
     - path: reports/pancreas_model2/vector_field.pdf
-      md5: 9bc1e12b5a2052934cbf0d902b81a257
+      md5: 14b03bce11c2799dc7d79121c16cc317
       size: 397596
     - path: reports/pancreas_model2/vector_field.pdf.png
       md5: 2bff17b5b0187728de366ba4f0b02cd3
       size: 698541
     - path: reports/pancreas_model2/volcano.pdf
-      md5: dff1dbf4abfbd65b5271add2d8bee563
+      md5: 9bf7cf363b6b27a9eca5a6b9f59ffa62
       size: 38346
     - path: reports/pancreas_model2/volcano.pdf.png
       md5: dcd4bad6fb0f085d8ff048521eb0b4f2
@@ -2042,8 +2043,8 @@ stages:
       md5: 73382ce8ef30d9575757f061a74ecb18
       size: 2263902602
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -2061,6 +2062,7 @@ stages:
           uncertainty_param_plot: reports/pbmc68k_model2/param_uncertainties.pdf
           vector_field_plot: reports/pbmc68k_model2/vector_field.pdf
           posterior_phase_portraits: reports/pbmc68k_model2/posterior_phase_portraits
+          t0_selection: reports/pbmc68k_model2/t0_selection.tif
           biomarker_selection_plot: reports/pbmc68k_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/pbmc68k_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/pbmc68k_model2/fig2_part1_plot.pdf
@@ -2072,56 +2074,56 @@ stages:
       md5: dc17c1ef835c7500d0b694422481fbd1
       size: 38352654
     - path: reports/pbmc68k_model2/clusters_violin_lin.pdf
-      md5: b933e09092250f24971d1e6c8fd8e12e
+      md5: a93e4c01e6a36bd9d518be3a971a6e96
       size: 163865
     - path: reports/pbmc68k_model2/clusters_violin_lin.pdf.png
       md5: cbdc19ab48ba9d4063e74d852c9f103f
       size: 2460186
     - path: reports/pbmc68k_model2/clusters_violin_log.pdf
-      md5: 3f700d471de9cb9d6049ff5ed3489198
+      md5: 0a3062a3347f1b6a5c4383a16a1ad47b
       size: 167073
     - path: reports/pbmc68k_model2/clusters_violin_log.pdf.png
       md5: bcdf46e8f26d1e4f545bd553ce618aa6
       size: 2688487
     - path: reports/pbmc68k_model2/fig2_part1_plot.pdf
-      md5: bbf976bd73dd73b1cc0a5d5a81bfc230
+      md5: 29a89794fa580c682b06f3bdb35397e0
       size: 4364577
     - path: reports/pbmc68k_model2/fig2_part1_plot.pdf.png
       md5: 209f6d9288a71e44199f2eba4722b80f
       size: 815723
     - path: reports/pbmc68k_model2/fig2_part2_plot.pdf
-      md5: b084fc647ce4db33ee9d966695a613ad
+      md5: 9f0d3a13e6dfcad50e89a3cfb5a4503c
       size: 21750906
     - path: reports/pbmc68k_model2/fig2_part2_plot.pdf.png
       md5: 91c659445824b9446200e7fd40b5924e
       size: 880548
     - path: reports/pbmc68k_model2/param_uncertainties.pdf
-      md5: 136ed21df81f72400bd97f06f342c5ed
-      size: 136484
+      md5: 1823b84e6ebe3c2844ffdb304b874f5f
+      size: 139420
     - path: reports/pbmc68k_model2/param_uncertainties.pdf.png
-      md5: d1a60baf8e0f55a544fc84354e672681
-      size: 757489
+      md5: 72c1ccaaaae6e83a1d50afbab60a2e9f
+      size: 857317
     - path: reports/pbmc68k_model2/rainbow.pdf
-      md5: f594863bc29e8dd28ef9588d4eeb4233
-      size: 94976685
+      md5: bee1d254ab8b1e332f34759901b03919
+      size: 94508392
     - path: reports/pbmc68k_model2/rainbow.pdf.png
-      md5: 76baed30cc60a87c820f1ed1f9d002f1
-      size: 2013204
+      md5: 1c6d808ad9fe3e88e3b11045e94323be
+      size: 2144226
     - path: reports/pbmc68k_model2/shared_time.pdf
-      md5: 849fb7f9628b28b84b795e2a5c5191c6
+      md5: 2f0ebee5f1285d28d1ee2e06355c361d
       size: 210524
     - path: reports/pbmc68k_model2/vector_field.pdf
-      md5: 4e18b09717fc6c1c8fbdb84c9c5c7e6b
+      md5: 1ad6eecf32178986b87ed18dd21d6397
       size: 1033561
     - path: reports/pbmc68k_model2/vector_field.pdf.png
       md5: 995204937711bf1c6932fde14ba1d59c
       size: 1196338
     - path: reports/pbmc68k_model2/volcano.pdf
-      md5: f89fb29b2c905ba3a6bb5b70bd6d50d3
-      size: 34583
+      md5: 15cd9f61c42057a3ae17e1dac1425eb1
+      size: 36783
     - path: reports/pbmc68k_model2/volcano.pdf.png
-      md5: c9377d59ac267bd940bb0f4d08b26593
-      size: 353624
+      md5: 6ca9a2aa15097480421e3cd5311c2aa3
+      size: 353603
   summarize@pons_model2:
     cmd: /usr/bin/time -v python summarize.py train_models=[pons_model2]
     deps:
@@ -2132,8 +2134,8 @@ stages:
       md5: a566defb5aa1968939cbe740184014ca
       size: 859080859
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -2151,6 +2153,7 @@ stages:
           uncertainty_param_plot: reports/pons_model2/param_uncertainties.pdf
           vector_field_plot: reports/pons_model2/vector_field.pdf
           posterior_phase_portraits: reports/pons_model2/posterior_phase_portraits
+          t0_selection: reports/pons_model2/t0_selection.tif
           biomarker_selection_plot: reports/pons_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/pons_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/pons_model2/fig2_part1_plot.pdf
@@ -2162,52 +2165,52 @@ stages:
       md5: b17eb7eaadc357d32ae68e3c30ee33f4
       size: 20173882
     - path: reports/pons_model2/clusters_violin_lin.pdf
-      md5: a638e4ed07484ac34ec0f2a34bc7e8fa
+      md5: e34ef1a23bd3540cdbe49ea9065adce8
       size: 72293
     - path: reports/pons_model2/clusters_violin_lin.pdf.png
       md5: e8d0f8d080d0e89cb21a276878c9c831
       size: 1749195
     - path: reports/pons_model2/clusters_violin_log.pdf
-      md5: dacfd9800b2d99e1cf731481fec16334
+      md5: 384d7ecce5ebf9416a7777db4b4e4c0f
       size: 72547
     - path: reports/pons_model2/clusters_violin_log.pdf.png
       md5: 7830cb2d8b422016d3754f940e7d77f1
       size: 1831635
     - path: reports/pons_model2/fig2_part1_plot.pdf
-      md5: 404a3d350485386a367157d0d9905dc1
+      md5: 37df82a2ab285866236afe398424045d
       size: 601195
     - path: reports/pons_model2/fig2_part1_plot.pdf.png
       md5: 38c6848240073b04adc0a90c36215392
       size: 637532
     - path: reports/pons_model2/fig2_part2_plot.pdf
-      md5: 6d0e80a1a687e485f53c892bc45a8e91
+      md5: d5c994cd26a88f5bfbcaca3e7c6fb2ec
       size: 2092120
     - path: reports/pons_model2/fig2_part2_plot.pdf.png
       md5: f97e47cd33380caff8011f213ad14788
       size: 695197
     - path: reports/pons_model2/param_uncertainties.pdf
-      md5: 3a3af62e44b9f7c377419f05eabfd176
+      md5: 2c6339975e927896a2de4d8cea2b3766
       size: 140098
     - path: reports/pons_model2/param_uncertainties.pdf.png
       md5: fbb4d255a8d6dc6374dbad073c2603d8
       size: 905995
     - path: reports/pons_model2/rainbow.pdf
-      md5: 861e1cc1144ef233883ba0cac0402212
+      md5: 588a7c447770e1b7a8334e59094c5079
       size: 8732898
     - path: reports/pons_model2/rainbow.pdf.png
       md5: 3342962a37537da8712babedb45148e7
       size: 1357455
     - path: reports/pons_model2/shared_time.pdf
-      md5: c7919b459195921bb9583f9a7151d544
+      md5: ac8a5dfb46d83145ad4ec9b771f97542
       size: 314031
     - path: reports/pons_model2/vector_field.pdf
-      md5: b5197689990346a35d1a8ef9ed0b48d6
+      md5: 5404bf363ac1af9f56aa31b8510181d2
       size: 377129
     - path: reports/pons_model2/vector_field.pdf.png
       md5: c4d786ee4e5c1b0dd6a690d0660e7858
       size: 798076
     - path: reports/pons_model2/volcano.pdf
-      md5: 3e74635c7588b663bfd059045daacb6d
+      md5: 30d9c977c5e5f778148b149dbad85409
       size: 37547
     - path: reports/pons_model2/volcano.pdf.png
       md5: 5ab65103d579376aac062977d5caeb3d
@@ -2222,8 +2225,8 @@ stages:
       md5: e7802daca9b8679c586e3977420daacf
       size: 1737302789
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -2241,6 +2244,7 @@ stages:
           uncertainty_param_plot: reports/pbmc10k_model2/param_uncertainties.pdf
           vector_field_plot: reports/pbmc10k_model2/vector_field.pdf
           posterior_phase_portraits: reports/pbmc10k_model2/posterior_phase_portraits
+          t0_selection: reports/pbmc10k_model2/t0_selection.tif
           biomarker_selection_plot: reports/pbmc10k_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/pbmc10k_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/pbmc10k_model2/fig2_part1_plot.pdf
@@ -2252,56 +2256,56 @@ stages:
       md5: a188f88c6bc8d6de79708712d5ec9b9d
       size: 37582371
     - path: reports/pbmc10k_model2/clusters_violin_lin.pdf
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+      md5: eeec3780fd54d2e8c2723e7f3789aa02
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   summarize@larry_tips_model2:
     cmd: /usr/bin/time -v python summarize.py train_models=[larry_tips_model2]
     deps:
@@ -2312,8 +2316,8 @@ stages:
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       size: 2376025578
     - path: summarize.py
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+      md5: 66d88b3802c50d56ce263008385a60b1
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     params:
       config.yaml:
         base:
@@ -2331,6 +2335,7 @@ stages:
           uncertainty_param_plot: reports/larry_tips_model2/param_uncertainties.pdf
           vector_field_plot: reports/larry_tips_model2/vector_field.pdf
           posterior_phase_portraits: reports/larry_tips_model2/posterior_phase_portraits
+          t0_selection: reports/larry_tips_model2/t0_selection.tif
           biomarker_selection_plot: reports/larry_tips_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/larry_tips_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/larry_tips_model2/fig2_part1_plot.pdf
@@ -2342,52 +2347,52 @@ stages:
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       size: 50020146
     - path: reports/larry_tips_model2/clusters_violin_lin.pdf
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     - path: reports/larry_tips_model2/fig2_part2_plot.pdf
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     - path: reports/larry_tips_model2/param_uncertainties.pdf
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     - path: reports/larry_tips_model2/rainbow.pdf
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     - path: reports/larry_tips_model2/shared_time.pdf
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       size: 269075
     - path: reports/larry_tips_model2/vector_field.pdf
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+      md5: c9ff3d97cc6c56a79b113a82311d5fb6
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     - path: reports/larry_tips_model2/vector_field.pdf.png
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     - path: reports/larry_tips_model2/volcano.pdf.png
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@@ -2664,8 +2669,8 @@ stages:
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       size: 6320835070
     - path: summarize.py
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+      md5: 66d88b3802c50d56ce263008385a60b1
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     params:
       config.yaml:
         base:
@@ -2683,6 +2688,7 @@ stages:
           uncertainty_param_plot: reports/larry_model2/param_uncertainties.pdf
           vector_field_plot: reports/larry_model2/vector_field.pdf
           posterior_phase_portraits: reports/larry_model2/posterior_phase_portraits
+          t0_selection: reports/larry_model2/t0_selection.tif
           biomarker_selection_plot: reports/larry_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/larry_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/larry_model2/fig2_part1_plot.pdf
@@ -2694,52 +2700,52 @@ stages:
       md5: 91a40d3791dce553689481b4d6c3ad2d
       size: 130451734
     - path: reports/larry_model2/clusters_violin_lin.pdf
-      md5: 2e5afb03198ab110b27367ff1395d120
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     - path: reports/larry_model2/fig2_part2_plot.pdf
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     - path: reports/larry_model2/param_uncertainties.pdf
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     - path: reports/larry_model2/rainbow.pdf
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       size: 68071944
     - path: reports/larry_model2/rainbow.pdf.png
       md5: c47beefa95ad047a1bd3d5c18f2267e4
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     - path: reports/larry_model2/shared_time.pdf
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+      md5: 4bffa59ebd1a4d49ad8feef83e99c5b4
       size: 227427
     - path: reports/larry_model2/vector_field.pdf
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     - path: reports/larry_model2/vector_field.pdf.png
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       size: 751219
     - path: reports/larry_model2/volcano.pdf
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       size: 35784
     - path: reports/larry_model2/volcano.pdf.png
       md5: 3210ebf81368790242ec5a00145f1224
@@ -2797,8 +2803,8 @@ stages:
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       size: 128091984
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
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+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -2816,6 +2822,7 @@ stages:
           uncertainty_param_plot: reports/larry_mono_model2/param_uncertainties.pdf
           vector_field_plot: reports/larry_mono_model2/vector_field.pdf
           posterior_phase_portraits: reports/larry_mono_model2/posterior_phase_portraits
+          t0_selection: reports/larry_mono_model2/t0_selection.tif
           biomarker_selection_plot: reports/larry_mono_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/larry_mono_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/larry_mono_model2/fig2_part1_plot.pdf
@@ -2827,52 +2834,52 @@ stages:
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       size: 2980125
     - path: reports/larry_mono_model2/clusters_violin_lin.pdf
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     - path: reports/larry_mono_model2/fig2_part2_plot.pdf
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     - path: reports/larry_mono_model2/rainbow.pdf
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     - path: reports/larry_mono_model2/rainbow.pdf.png
       md5: a22ad72da0401b86db6b13666a0070e4
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     - path: reports/larry_mono_model2/shared_time.pdf
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     - path: reports/larry_mono_model2/vector_field.pdf
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     - path: reports/larry_mono_model2/vector_field.pdf.png
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     - path: reports/larry_mono_model2/volcano.pdf
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     - path: reports/larry_mono_model2/volcano.pdf.png
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@@ -2887,8 +2894,8 @@ stages:
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       size: 105880284
     - path: summarize.py
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+      md5: 66d88b3802c50d56ce263008385a60b1
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     params:
       config.yaml:
         base:
@@ -2906,6 +2913,7 @@ stages:
           uncertainty_param_plot: reports/larry_neu_model2/param_uncertainties.pdf
           vector_field_plot: reports/larry_neu_model2/vector_field.pdf
           posterior_phase_portraits: reports/larry_neu_model2/posterior_phase_portraits
+          t0_selection: reports/larry_neu_model2/t0_selection.tif
           biomarker_selection_plot: reports/larry_neu_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/larry_neu_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/larry_neu_model2/fig2_part1_plot.pdf
@@ -2917,52 +2925,52 @@ stages:
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     - path: reports/larry_neu_model2/clusters_violin_lin.pdf
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     - path: reports/larry_neu_model2/shared_time.pdf
-      md5: 21b6f851e41c28757a990ca2beac468a
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     - path: reports/larry_neu_model2/vector_field.pdf
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       md5: 0fbc1da72810af8c70398a50435e2f4c
@@ -2977,8 +2985,8 @@ stages:
       md5: 324c410d940e5b11d29f02566d51c12a
       size: 334119477
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -2996,6 +3004,7 @@ stages:
           uncertainty_param_plot: reports/larry_multilineage_model2/param_uncertainties.pdf
           vector_field_plot: reports/larry_multilineage_model2/vector_field.pdf
           posterior_phase_portraits: reports/larry_multilineage_model2/posterior_phase_portraits
+          t0_selection: reports/larry_multilineage_model2/t0_selection.tif
           biomarker_selection_plot: reports/larry_multilineage_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/larry_multilineage_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/larry_multilineage_model2/fig2_part1_plot.pdf
@@ -3007,52 +3016,52 @@ stages:
       md5: 1efb5851d7c9f7038989d12564ddc48b
       size: 7714181
     - path: reports/larry_multilineage_model2/clusters_violin_lin.pdf
-      md5: 7b5cb557f5abf44054673a4cad6847a1
+      md5: 374371e5195579a07b93041b421e05fe
       size: 84395
     - path: reports/larry_multilineage_model2/clusters_violin_lin.pdf.png
       md5: cb60ac99eefa62b7cbc745c8c807b2c5
       size: 1459255
     - path: reports/larry_multilineage_model2/clusters_violin_log.pdf
-      md5: c853b72be461442b713877a7529d50e6
+      md5: cfa0d25bf90ca5a66bf265d4afd1ebb8
       size: 84339
     - path: reports/larry_multilineage_model2/clusters_violin_log.pdf.png
       md5: 4873bb44a85c03173a1ffe2b11f022aa
       size: 1555454
     - path: reports/larry_multilineage_model2/fig2_part1_plot.pdf
-      md5: 3175a50943a9324cfae80409de23199d
+      md5: 35f24ac73776ddd60a7033850f0b4835
       size: 289657
     - path: reports/larry_multilineage_model2/fig2_part1_plot.pdf.png
       md5: b2295ed0ceaddb79ae230c6c41865f53
       size: 441102
     - path: reports/larry_multilineage_model2/fig2_part2_plot.pdf
-      md5: 4449d4fe7a71372b4f06b33d8a10ea31
+      md5: 5a3e8006f7542c1b410b03ea51589b69
       size: 763051
     - path: reports/larry_multilineage_model2/fig2_part2_plot.pdf.png
       md5: bcef4cf00801d132893ea838864b6aa7
       size: 604761
     - path: reports/larry_multilineage_model2/param_uncertainties.pdf
-      md5: 155b083a071c9b7ff3e334e003d70ad8
+      md5: bbb8136ce1e54ac35e0c5a47d0c87839
       size: 140878
     - path: reports/larry_multilineage_model2/param_uncertainties.pdf.png
       md5: 11864fd58425b363b90cf0055e691034
       size: 1032216
     - path: reports/larry_multilineage_model2/rainbow.pdf
-      md5: cc00449bd917b2ac65b16e9b956c289c
+      md5: d42a27106e1643a6ae9931cc6fdb088e
       size: 3334285
     - path: reports/larry_multilineage_model2/rainbow.pdf.png
       md5: 8a23b764db38829e4851f63e40147c92
       size: 1645854
     - path: reports/larry_multilineage_model2/shared_time.pdf
-      md5: b87ac5931961a27ad4deff368eba9505
+      md5: f84301ef9ed4e52c1252bb315d55a95e
       size: 140815
     - path: reports/larry_multilineage_model2/vector_field.pdf
-      md5: c32b17157465d3dfc175b3abf7008554
+      md5: 986fcf6cec3ab4233aa131d1045af8c0
       size: 207973
     - path: reports/larry_multilineage_model2/vector_field.pdf.png
       md5: 917b84813baf08df1c28dd599127cc18
       size: 481176
     - path: reports/larry_multilineage_model2/volcano.pdf
-      md5: 8d822beea7f65990ad2ab199861b118e
+      md5: 3246650d6eda607f3f7e2884b86069a0
       size: 36996
     - path: reports/larry_multilineage_model2/volcano.pdf.png
       md5: 74e31a018fc069f65a5317a4cdf4dc86
@@ -3473,8 +3482,8 @@ stages:
       md5: 5c0d598b6ce53d54015e4abaf4954fb1
       size: 760341824
     - path: summarize.py
-      md5: d42d6ccbd1c16e746c726a6e2c9cfc2f
-      size: 27880
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -3491,6 +3500,8 @@ stages:
           rainbow_plot: reports/bonemarrow_model2/rainbow.pdf
           uncertainty_param_plot: reports/bonemarrow_model2/param_uncertainties.pdf
           vector_field_plot: reports/bonemarrow_model2/vector_field.pdf
+          posterior_phase_portraits: reports/bonemarrow_model2/posterior_phase_portraits
+          t0_selection: reports/bonemarrow_model2/t0_selection.tif
           biomarker_selection_plot: reports/bonemarrow_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/bonemarrow_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/bonemarrow_model2/fig2_part1_plot.pdf
@@ -3502,52 +3513,52 @@ stages:
       md5: ab00ad34356484260492e66b2ad8f912
       size: 17615324
     - path: reports/bonemarrow_model2/clusters_violin_lin.pdf
-      md5: 9068dc30cd683c9d00cfadb7fc563022
+      md5: 6c18ea9c1251b6d93af431c247b405e1
       size: 150717
     - path: reports/bonemarrow_model2/clusters_violin_lin.pdf.png
       md5: 6fd43e195a753036b028a38813e32bef
       size: 2316012
     - path: reports/bonemarrow_model2/clusters_violin_log.pdf
-      md5: d674a37e253566b9533b52cb0a1c930d
+      md5: 6908fd94a2312840be41cb25bc8d5924
       size: 151467
     - path: reports/bonemarrow_model2/clusters_violin_log.pdf.png
       md5: a846cc0d014b0563216e15eab71dafd7
       size: 2485038
     - path: reports/bonemarrow_model2/fig2_part1_plot.pdf
-      md5: 9e77d680f39a41dac3943f049bd498d0
+      md5: bea2349a28bedfc52d1417c458da1f65
       size: 486075
     - path: reports/bonemarrow_model2/fig2_part1_plot.pdf.png
       md5: fa9af7dd5356dc410c07c7c8b09820a4
       size: 418493
     - path: reports/bonemarrow_model2/fig2_part2_plot.pdf
-      md5: b694bf93944e3a80d7ad810a41f2b9c1
+      md5: 62103d11a0074c9db070f66251f22bf2
       size: 1931458
     - path: reports/bonemarrow_model2/fig2_part2_plot.pdf.png
       md5: 682373901caf02aba63df837ce79f68a
       size: 511903
     - path: reports/bonemarrow_model2/param_uncertainties.pdf
-      md5: 1ce1edf70061328166e0558975306448
+      md5: 516e4b332f644f643900a5cb7b95ea47
       size: 138685
     - path: reports/bonemarrow_model2/param_uncertainties.pdf.png
       md5: 361fca5e5f00f0ccaf95c4005266cc56
       size: 809961
     - path: reports/bonemarrow_model2/rainbow.pdf
-      md5: 4c56b631bdda62c987525dc85c44e39f
+      md5: 5e7444a9c898500836f49eabf925cd03
       size: 8157744
     - path: reports/bonemarrow_model2/rainbow.pdf.png
       md5: 98ad0cd2b66713d37d26b4258949f171
       size: 1112702
     - path: reports/bonemarrow_model2/shared_time.pdf
-      md5: 90350eb65d1ba2d97a607a1a73b90111
+      md5: a7c9deb906aff00a468e3f0086b636f1
       size: 168622
     - path: reports/bonemarrow_model2/vector_field.pdf
-      md5: 9780386159349e913b36b64f2b0ee916
+      md5: 48549a886e23a6a72ec8ae857689ee70
       size: 320629
     - path: reports/bonemarrow_model2/vector_field.pdf.png
       md5: d4511e2cf1ff27bff8d9b48348438aad
       size: 463204
     - path: reports/bonemarrow_model2/volcano.pdf
-      md5: 781565d48fd61e0e2fee282a61e743b4
+      md5: c500b8da60d1aac06382d8bd467a4678
       size: 40856
     - path: reports/bonemarrow_model2/volcano.pdf.png
       md5: 860edac120b7ab2fb4be67aa1bbb4e38
@@ -3756,8 +3767,8 @@ stages:
       md5: 7392ed14357bc9409ec63f1820a02b96
       size: 587927873
     - path: summarize.py
-      md5: 6827eaef68101af8db5d8b5c7d9f5f0e
-      size: 34841
+      md5: 66d88b3802c50d56ce263008385a60b1
+      size: 39519
     params:
       config.yaml:
         base:
@@ -3775,6 +3786,7 @@ stages:
           uncertainty_param_plot: reports/pbmc5k_model2/param_uncertainties.pdf
           vector_field_plot: reports/pbmc5k_model2/vector_field.pdf
           posterior_phase_portraits: reports/pbmc5k_model2/posterior_phase_portraits
+          t0_selection: reports/pbmc5k_model2/t0_selection.tif
           biomarker_selection_plot: reports/pbmc5k_model2/markers_selection_scatterplot.tif
           biomarker_phaseportrait_plot: reports/pbmc5k_model2/markers_phaseportrait.pdf
           fig2_part1_plot: reports/pbmc5k_model2/fig2_part1_plot.pdf
@@ -3786,52 +3798,52 @@ stages:
       md5: 14078b803a0d70bfff0b655357081857
       size: 13338832
     - path: reports/pbmc5k_model2/clusters_violin_lin.pdf
-      md5: d0dae531151663767ee605a8316b4f46
+      md5: 2e2f55dc2a03331a24dbe4b0f80ea7dc
       size: 139290
     - path: reports/pbmc5k_model2/clusters_violin_lin.pdf.png
       md5: c4b43b9ae2f089a949524dd89fba9c7b
       size: 2275202
     - path: reports/pbmc5k_model2/clusters_violin_log.pdf
-      md5: 2497609f4d0069a294d2a0ae16583051
+      md5: 963adc89c0115be697dd39050c49197d
       size: 140082
     - path: reports/pbmc5k_model2/clusters_violin_log.pdf.png
       md5: ab47848b71f1944ee25c77c4fd9f0905
       size: 2299584
     - path: reports/pbmc5k_model2/fig2_part1_plot.pdf
-      md5: 1fa05e9a7e81014bb111687bde092498
+      md5: eac79bd00a32af28d3c475ef0bccbac7
       size: 461666
     - path: reports/pbmc5k_model2/fig2_part1_plot.pdf.png
       md5: 2e050bf87ce6d7e04f43b403d887020b
       size: 680867
     - path: reports/pbmc5k_model2/fig2_part2_plot.pdf
-      md5: 50d381ecc8e4aaec0fcc477c3bece173
+      md5: 3e69808ad2fc52d94e6ef6f8919b0c67
       size: 1290446
     - path: reports/pbmc5k_model2/fig2_part2_plot.pdf.png
       md5: 4f82d40b12facc97c4d15ec0d527aa37
       size: 699550
     - path: reports/pbmc5k_model2/param_uncertainties.pdf
-      md5: b45ea80eab564d53de2aa3e998292ec8
+      md5: 4035e06a4fb3ed41f3de61cc27339555
       size: 138835
     - path: reports/pbmc5k_model2/param_uncertainties.pdf.png
       md5: 9a29ce4d8bd25ba206e6314cfc3ab99b
       size: 891813
     - path: reports/pbmc5k_model2/rainbow.pdf
-      md5: 0f7046be273fa576fedb6acabd9b977d
+      md5: e39978306225184e1964e0fce1c7d787
       size: 5349095
     - path: reports/pbmc5k_model2/rainbow.pdf.png
       md5: 2edd2ab88641b17344b3b48f92c1fe8d
       size: 1353259
     - path: reports/pbmc5k_model2/shared_time.pdf
-      md5: 280a4bb74236c79b3e955d18cab87da2
+      md5: 80252b39d62e1bc1ec3b2026c7e37202
       size: 328510
     - path: reports/pbmc5k_model2/vector_field.pdf
-      md5: 9b5ab9f2861b33c1766e469f15300e99
+      md5: edaf21ac9502358f9417288a4fbb1100
       size: 469148
     - path: reports/pbmc5k_model2/vector_field.pdf.png
       md5: e212774fb78d2642f89960d9d0dcf749
       size: 820922
     - path: reports/pbmc5k_model2/volcano.pdf
-      md5: 9d6567f815c203114fc904fa5f74fd5b
+      md5: 51f345278ba68ab03b34faa186080ea7
       size: 37846
     - path: reports/pbmc5k_model2/volcano.pdf.png
       md5: 5e46acacf3e24deeff7b2dd0c896d692
diff --git a/reproducibility/figures/summarize.py b/reproducibility/figures/summarize.py
index 30908ab03..4fd7870c2 100644
--- a/reproducibility/figures/summarize.py
+++ b/reproducibility/figures/summarize.py
@@ -512,7 +512,7 @@ def plot_parameter_posterior_distributions(
 
 
 def extrapolate_prediction_sample_predictive(
-    data_model_conf, adata, grid_time_points=500
+    data_model_conf, adata, grid_time_points=1000
 ):
     pyrovelocity_model_path = data_model_conf.model_path
     PyroVelocity.setup_anndata(adata)
@@ -545,9 +545,6 @@ def extrapolate_prediction_sample_predictive(
                 axis=-3,
             )
         ).to("cuda:0")
-    for key in posterior_samples:
-        print(posterior_samples[key].shape)
-    print("-------")
     dummy_obs = (
         torch.ones((1, adata.shape[1])).to("cuda:0"),
         torch.ones((1, adata.shape[1])).to("cuda:0"),
@@ -580,17 +577,26 @@ def extrapolate_prediction_sample_predictive(
             ),
             posterior_samples=posterior_samples,
         )(*dummy_obs)
-        # print(test['cell_gene_state'])
-        # print(test['cell_time'])
+        print(test.keys())
         grid_time_samples_ut.append(test["ut"])
         grid_time_samples_st.append(test["st"])
         grid_time_samples_state.append(test["cell_gene_state"])
     grid_time_samples_ut = torch.cat(grid_time_samples_ut, dim=-2)
     grid_time_samples_st = torch.cat(grid_time_samples_st, dim=-2)
+    grid_time_samples_u0 = posterior_samples["u_offset"]
+    grid_time_samples_s0 = posterior_samples["s_offset"]
+    grid_time_samples_uinf = test["u_inf"]
+    grid_time_samples_sinf = test["s_inf"]
+    grid_time_samples_uscale = posterior_samples["u_scale"]
     grid_time_samples_state = torch.cat(grid_time_samples_state, dim=-2)
     return (
         grid_time_samples_ut.cpu().detach().numpy(),
         grid_time_samples_st.cpu().detach().numpy(),
+        grid_time_samples_u0.cpu().detach().numpy(),
+        grid_time_samples_s0.cpu().detach().numpy(),
+        grid_time_samples_uinf.cpu().detach().numpy(),
+        grid_time_samples_sinf.cpu().detach().numpy(),
+        grid_time_samples_uscale.cpu().detach().numpy(),
         grid_time_samples_state.cpu().detach().numpy(),
     )
 
@@ -601,8 +607,7 @@ def extrapolate_prediction_trace(data_model_conf, adata, grid_time_points=500):
     model = PyroVelocity(adata)
     model = model.load_model(pyrovelocity_model_path, adata, use_gpu=0)
     # grid_cell_time = torch.linspace(-10, 20, grid_time_points)
-    grid_cell_time = torch.linspace(0.01, 50, grid_time_points)
-    print(grid_cell_time.shape)
+    grid_cell_time = torch.linspace(-10, 100, grid_time_points)
     dummy_obs = (
         torch.ones((1, adata.shape[1])),
         torch.ones((1, adata.shape[1])),
@@ -638,6 +643,11 @@ def posterior_curve(
     posterior_samples,
     grid_time_samples_ut,
     grid_time_samples_st,
+    grid_time_samples_u0,
+    grid_time_samples_s0,
+    grid_time_samples_uinf,
+    grid_time_samples_sinf,
+    grid_time_samples_uscale,
     grid_time_samples_state,
     gene_set,
     dataset,
@@ -647,9 +657,14 @@ def posterior_curve(
     for figi, gene in enumerate(gene_set):
         (index,) = np.where(adata.var_names == gene)
         fig, ax = plt.subplots(4, 5)
-        fig.set_size_inches(18, 12)
+        fig.set_size_inches(15, 10)
         ax = ax.flatten()
         for sample in range(20):
+            t0_sample = posterior_samples["t0"][sample][:, index[0]].flatten()
+            cell_time_sample_max = (
+                posterior_samples["cell_time"][sample].flatten().max()
+            )
+            cell_time_sample = posterior_samples["cell_time"][sample].flatten()
             ax[sample].scatter(
                 posterior_samples["st_mean"][:, index[0]],
                 posterior_samples["ut_mean"][:, index[0]],
@@ -661,20 +676,56 @@ def posterior_curve(
             im = ax[sample].scatter(
                 grid_time_samples_st[sample][:, index[0]],
                 grid_time_samples_ut[sample][:, index[0]],
-                s=10,
+                s=13,
                 marker="o",
                 linewidth=0,
                 c=grid_time_samples_state[sample][:, index[0]],
             )
+
+            u0 = grid_time_samples_u0[sample][:, index[0]].flatten()
+            uscale = grid_time_samples_uscale[sample][:, index[0]].flatten()
+            s0 = grid_time_samples_s0[sample][:, index[0]].flatten()
+            print(gene, u0, s0)
+            u_inf = grid_time_samples_uinf[sample][:, index[0]].flatten()
+            s_inf = grid_time_samples_sinf[sample][:, index[0]].flatten()
+            print(gene, u_inf, s_inf)
+
+            # u0 = posterior_samples['u_offset'][sample][:, index[0]].flatten()
+            # s0 = posterior_samples['s_offset'][sample][:, index[0]].flatten()
+            # u_inf = posterior_samples['u_inf'][sample][:, index[0]].flatten()
+            # s_inf = posterior_samples['s_inf'][sample][:, index[0]].flatten()
+            ax[sample].scatter(
+                s0, u0 * uscale, s=60, marker="p", linewidth=0.5, c="purple"
+            )
+            ax[sample].scatter(
+                s_inf, u_inf * uscale, s=60, marker="p", linewidth=0.5, c="black"
+            )
             # ax[sample].plot(grid_time_samples_st[sample][:, index[0]],
             #                grid_time_samples_ut[sample][:, index[0]],
             #                linestyle="--", linewidth=3, color='g')
-            ax[sample].set_title(f"{gene} model 2 sample {sample}")
+            ax[sample].set_title(
+                f"{gene} model 2 sample {sample}\nt0>celltime:{(t0_sample>cell_time_sample_max)} {(t0_sample>cell_time_sample).sum()}",
+                fontsize=6.5,
+            )
             ax[sample].set_xlim(
-                0, np.max(posterior_samples["st_mean"][:, index[0]]) * 1.1
+                0,
+                max(
+                    [
+                        np.max(posterior_samples["st_mean"][:, index[0]]) * 1.1,
+                        s0 * 1.1,
+                        s_inf * 1.1,
+                    ]
+                ),
             )
             ax[sample].set_ylim(
-                0, np.max(posterior_samples["ut_mean"][:, index[0]]) * 1.1
+                0,
+                max(
+                    [
+                        np.max(posterior_samples["ut_mean"][:, index[0]]) * 1.1,
+                        u0 * uscale * 1.1,
+                        u_inf * uscale * 1.05,
+                    ]
+                ),
             )
             fig.colorbar(im, ax=ax[sample])
         fig.tight_layout()
@@ -755,10 +806,67 @@ def plots(conf: DictConfig, logger: Logger) -> None:
 
         logger.info(f"Loading pyrovelocity data: {pyrovelocity_data_path}")
         posterior_samples = CompressedPickle.load(pyrovelocity_data_path)
+        print(posterior_samples.keys())
+
+        fig, ax = plt.subplots(5, 6)
+        fig.set_size_inches(26, 24)
+        ax = ax.flatten()
+        for sample in range(29):
+            t0_sample = posterior_samples["t0"][sample]
+            switching_sample = posterior_samples["switching"][sample]
+            cell_time_sample = posterior_samples["cell_time"][sample]
+            print(t0_sample.shape)
+            print(cell_time_sample)
+            ax[sample].scatter(
+                t0_sample.flatten(),
+                2 * np.ones(t0_sample.shape[-1]),
+                s=1,
+                c="red",
+                label="t0",
+            )
+            ax[sample].scatter(
+                switching_sample.flatten(),
+                3 * np.ones(t0_sample.shape[-1]),
+                s=1,
+                c="purple",
+                label="switching",
+            )
+            ax[sample].scatter(
+                cell_time_sample.flatten(),
+                np.ones(cell_time_sample.shape[0]),
+                s=1,
+                c="blue",
+                label="shared time",
+            )
+            ax[sample].set_ylim(-0.5, 4)
+            if sample == 28:
+                ax[sample].legend(loc="best", bbox_to_anchor=(0.5, 0.0, 0.5, 0.5))
+            print((t0_sample.flatten() > cell_time_sample.flatten().max()).sum())
+            print((t0_sample.flatten() < switching_sample.flatten().max()).sum())
+            print((t0_sample.flatten() > switching_sample.flatten().max()).sum())
+            for gene in adata.var_names[
+                t0_sample.flatten() > cell_time_sample.flatten().max()
+            ]:
+                print(gene)
+        ax[-1].hist(t0_sample.flatten(), bins=200, color="red", alpha=0.3)
+        ax[-1].hist(cell_time_sample.flatten(), bins=500, color="blue", alpha=0.3)
+
+        fig.savefig(
+            reports_data_model_conf.t0_selection,
+            facecolor=fig.get_facecolor(),
+            bbox_inches="tight",
+            edgecolor="none",
+            dpi=300,
+        )
 
         (
             grid_time_samples_ut,
             grid_time_samples_st,
+            grid_time_samples_u0,
+            grid_time_samples_s0,
+            grid_time_samples_uinf,
+            grid_time_samples_sinf,
+            grid_time_samples_uscale,
             grid_time_samples_state,
         ) = extrapolate_prediction_sample_predictive(
             data_model_conf, adata, grid_time_points=500
@@ -909,6 +1017,11 @@ def plots(conf: DictConfig, logger: Logger) -> None:
             posterior_samples,
             grid_time_samples_ut,
             grid_time_samples_st,
+            grid_time_samples_u0,
+            grid_time_samples_s0,
+            grid_time_samples_uinf,
+            grid_time_samples_sinf,
+            grid_time_samples_uscale,
             grid_time_samples_state,
             geneset,
             data_model,