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 0000000000000000000000000000000000000000..c27628ad6689b3ddcea86af0ad2d1960c401ec77 --- /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 Binary files /dev/null and b/11_Hypothesis_testing/exercise_embryos/automatic/RoiSet.zip differ 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 0000000000000000000000000000000000000000..f70a1b18811c53390d80ced0d4a52f91b965706a --- /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 0000000000000000000000000000000000000000..2616d1ab3c99b03a7027356c2319e778db4b6c85 --- /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 Binary files /dev/null and b/11_Hypothesis_testing/exercise_embryos/manual/RoiSet.zip differ