From 93f735639f4012599d0a9c60fdee0ceba109d4aa Mon Sep 17 00:00:00 2001
From: haesleinhuepf <rhaase@mpi-cbg.de>
Date: Sun, 14 Jun 2020 16:17:25 +0200
Subject: [PATCH] added exercise data

---
 .../exercise_embryos/automatic/Results.csv    |  34 +++++++++++++++
 .../exercise_embryos/automatic/RoiSet.zip     | Bin 0 -> 10965 bytes
 .../automatic/process_embryos.ijm             |  41 ++++++++++++++++++
 .../exercise_embryos/manual/Results.csv       |  27 ++++++++++++
 .../exercise_embryos/manual/RoiSet.zip        | Bin 0 -> 4252 bytes
 5 files changed, 102 insertions(+)
 create mode 100644 11_Hypothesis_testing/exercise_embryos/automatic/Results.csv
 create mode 100644 11_Hypothesis_testing/exercise_embryos/automatic/RoiSet.zip
 create mode 100644 11_Hypothesis_testing/exercise_embryos/automatic/process_embryos.ijm
 create mode 100644 11_Hypothesis_testing/exercise_embryos/manual/Results.csv
 create mode 100644 11_Hypothesis_testing/exercise_embryos/manual/RoiSet.zip

diff --git a/11_Hypothesis_testing/exercise_embryos/automatic/Results.csv b/11_Hypothesis_testing/exercise_embryos/automatic/Results.csv
new file mode 100644
index 0000000..c27628a
--- /dev/null
+++ b/11_Hypothesis_testing/exercise_embryos/automatic/Results.csv
@@ -0,0 +1,34 @@
+ ,Area
+1,3224
+2,3137
+3,2653
+4,2442
+5,1145
+6,2558
+7,2768
+8,1485
+9,2731
+10,2515
+11,2756
+12,2430
+13,3200
+14,2226
+15,3335
+16,132
+17,2196
+18,2668
+19,2897
+20,2952
+21,2913
+22,2897
+23,1353
+24,2061
+25,3103
+26,2860
+27,2618
+28,2639
+29,2113
+30,166
+31,155
+32,1827
+33,568
diff --git a/11_Hypothesis_testing/exercise_embryos/automatic/RoiSet.zip b/11_Hypothesis_testing/exercise_embryos/automatic/RoiSet.zip
new file mode 100644
index 0000000000000000000000000000000000000000..02420b9ab683985417178fec3123355f3ca328c9
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diff --git a/11_Hypothesis_testing/exercise_embryos/automatic/process_embryos.ijm b/11_Hypothesis_testing/exercise_embryos/automatic/process_embryos.ijm
new file mode 100644
index 0000000..f70a1b1
--- /dev/null
+++ b/11_Hypothesis_testing/exercise_embryos/automatic/process_embryos.ijm
@@ -0,0 +1,41 @@
+// clean up first
+run("Close All");
+roiManager("reset");
+
+// load sample data
+run("Embryos (42K)");
+
+// convert it to make it processable
+run("8-bit");
+
+// duplicate the image before we process it
+run("Duplicate...", " ");
+
+// blur it a bit to remove noise
+run("Gaussian Blur...", "sigma=2");
+setAutoThreshold("Default");
+
+// Segmentation
+setOption("BlackBackground", true);
+run("Convert to Mask");
+
+// Binary image postprocessing
+run("Fill Holes");
+run("Watershed");
+run("Erode");
+run("Erode");
+run("Erode");
+
+run("Dilate");
+run("Dilate");
+run("Dilate");
+
+// configure: area measurement
+run("Set Measurements...", "area redirect=None decimal=3");
+
+// measure area and show ROIs in ROI manager
+run("Analyze Particles...", "display add");
+
+// visualize results on original image
+close();
+roiManager("show all with labels");
\ No newline at end of file
diff --git a/11_Hypothesis_testing/exercise_embryos/manual/Results.csv b/11_Hypothesis_testing/exercise_embryos/manual/Results.csv
new file mode 100644
index 0000000..2616d1a
--- /dev/null
+++ b/11_Hypothesis_testing/exercise_embryos/manual/Results.csv
@@ -0,0 +1,27 @@
+ ,Area
+1,2128
+2,1640
+3,2828
+4,2560
+5,2560
+6,2644
+7,2368
+8,2632
+9,2468
+10,2672
+11,2552
+12,3124
+13,2536
+14,3016
+15,3620
+16,3308
+17,2552
+18,2732
+19,2732
+20,3532
+21,3124
+22,3532
+23,1648
+24,2732
+25,3176
+26,2732
diff --git a/11_Hypothesis_testing/exercise_embryos/manual/RoiSet.zip b/11_Hypothesis_testing/exercise_embryos/manual/RoiSet.zip
new file mode 100644
index 0000000000000000000000000000000000000000..351f9fd18d1f28dcfca5bbdbfc9e15ede0ff03a7
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literal 0
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-- 
GitLab