Add some useful links at the end

[max/ct_plotting.git] / slides.rst

diff --git a/slides.rst b/slides.rst
index 6b6b5b8250b96f682fcbc575046960de1f8549d8..acd4a56c8e25ab9aa85f5a9d1ab17f5c5c9cbb95 100644 (file)
--- a/slides.rst
+++ b/slides.rst
@@ -6,23 +6,47 @@ I am not a biologist, please stop me and correct me if I say silly things.
 Pod Width
 ---------
 
+.. image:: plot_bar_pod_widths.png
+   :width: 9cm
+
 Sphericity
 ----------
 
+.. image:: plot_bar_sphericities_of_seeds.png
+   :width: 9cm
+
 Volume
 ------
 
+.. image:: plot_bar_volumes_of_seeds.png
+   :width: 9cm
+
 Surface Area
 ------------
 
+.. image:: plot_bar_surface_area_of_seeds.png
+   :width: 9cm
+
 Correlations
 ------------
 
+.. image:: plot_correlations.png
+   :width: 8cm
+
+.. image:: plot_number_of_seeds_vs_mean_volume_of_seeds.png
+   :width: 9cm
+
+.. image:: plot_length_of_pod_vs_mean_volume_of_seeds.png
+   :width: 9cm
+
+.. image:: plot_length_of_pod_vs_number_of_seeds.png
+   :width: 9cm
+
 Filtering false seeds
 ---------------------
 
 .. image:: brassica_pod_lq.png
-   :width: 8cm
+   :width: 7.3cm
 
 * Image analysis produces many false seeds at the beak tip
 * Density and size is comparable to seed
@@ -36,13 +60,17 @@ Spine fitting
 * Fit X and Y position as cubic functions of z
 * Define 'real z' as the distance measured along the fitted curve from 
   the beak to the z coordinate of the point
-* TODO: Include picture of fitted curve
 
-Distinguishing between beak tip and Real Seeds™
------------------------------------------------
+.. image:: fitting_debug.svg
+   :target: https://git.friedersdorff.com/max/ct_plotting/raw/master/fitting_debug.gif
+   :width: 1.22cm
+
+
+Classify beak tip and Real Seeds™
+---------------------------------
 
 Failed approaches: 
-##################
+
 1. Assert that seeds must not be implausible - Removed insufficiently many seeds
 
    * Too close to the ends of the pod
@@ -65,7 +93,9 @@ Break at Minimum Kernel Density Estimation (KDE)
 * Beak has no Real Seeds™ and low density
 * Expect a gap in real z of detected seeds
 
+
 .. image:: plot_real_zs_genotype_unfiltered.png
+   :width: 11cm
 
 .. raw:: pdf
 
@@ -82,11 +112,36 @@ Break at Minimum Kernel Density Estimation (KDE)
 * Profit
 
 .. image:: plot_real_zs_genotype_filtered.png
+   :width: 11cm
+
+.. image:: plot_real_zs_genotype_unfiltered.png
+   :width: 11cm
 
 Beak and Silique length
 -----------------------
 
 Use the seed with lowest real z to mark the boundary of beak and silique:
 
-TODO: insert silique length and beak length graphs
+.. image:: plot_bar_silique_lengths.png
+.. image:: plot_bar_beak_lengths.png
+
+Resources
+---------
+
+`Git Repository`_
+
+`This Presentation`_
+
+`Numpy`_
+
+`Matplotlib`_
+
+`Seaborne`_
+
+.. _Git Repository: https://github.com/NPPC-UK/ct_scanner_plotting 
+.. _This Presentation: https://git.friedersdorff.com/max/ct_plotting.git
+.. _Numpy: https://www.numpy.org/
+.. _Matplotlib: https://matplotlib.org/
+.. _Seaborne: https://seaborn.pydata.org/
 
+.. target-notes::