segment_rgb/segment_rgb_short.md

+### This is the copy of my notebook segment_rgb.ipynb as of 27/03/2020
+
+
+
+```python
+fluo_path = '/Volumes/Multicell/Sebastien/mESC_aggregates/SUMO/SUMOICC/8001.nd2'
+```
+
+
+```python
+result = {'FOVs': {}}
+for i, w in enumerate(well):
+    print(f'Field of view {i+1}')
+    result['FOVs'][i] = segment_multichannel(w)
+
+```
+
+
+    {'x': 2048, 'y': 2044, 'c': 4, 'm': 8}
+    ['DaFiTr', 'FITC', 'TRITC', 'DAPI']
+    Field of view 1
+    3 regions
+
+
+
+![png](output_18_2.png)
+
+
+    2 after filtering
+    2 after filtering
+    2 after filtering
+    MAL 476.3633960441524, ecc 0.6699504946791014
+    MAL 555.2292799551585, ecc 0.7116636982699971
+    Field of view 2
+    5 regions
+
+
+
+![png](output_18_4.png)
+
+
+
+![png](output_18_5.png)
+
+
+
+![png](output_18_6.png)
+
+
+    2 after filtering
+    2 after filtering
+    2 after filtering
+    MAL 508.9015864625201, ecc 0.7707228793807227
+    MAL 347.1494245878248, ecc 0.5892010452302452
+    Field of view 3
+    5 regions
+
+
+
+![png](output_18_8.png)
+
+
+
+![png](output_18_9.png)
+
+
+
+![png](output_18_10.png)
+
+
+    1 after filtering
+    1 after filtering
+    1 after filtering
+    MAL 404.5591700143066, ecc 0.5922370293260343
+    Field of view 4
+    1 regions
+
+
+
+![png](output_18_12.png)
+
+
+
+![png](output_18_13.png)
+
+
+    0 after filtering
+    0 after filtering
+    0 after filtering
+    Field of view 5
+    1 regions
+
+
+
+![png](output_18_15.png)
+
+
+    0 after filtering
+    0 after filtering
+    0 after filtering
+    Field of view 6
+    14 regions
+
+
+
+![png](output_18_17.png)
+
+
+    0 after filtering
+    0 after filtering
+    0 after filtering
+    Field of view 7
+    14 regions
+
+
+
+![png](output_18_19.png)
+
+
+    0 after filtering
+    0 after filtering
+    0 after filtering
+    Field of view 8
+    7 regions
+
+
+
+![png](output_18_21.png)
+
+
+    2 after filtering
+    2 after filtering
+    2 after filtering
+    MAL 501.45720955763915, ecc 0.7736063195664731
+    MAL 343.1232805515898, ecc 0.6143762335628465
+
+
+
+![png](output_18_23.png)
+
+
+
+![png](output_18_24.png)
+
+
+
+```python
+r_profile = np.array(result['FOVs'][0]['organoids'][0]['intensity_profiles']['r']['max'])
+```
+
+
+```python
+subsample_intensity_profile(r_profile, plot=1)
+```
+
+
+
+
+    array([0.01352204, 0.30229415, 0.46431859, 0.59528279, 0.75710012,
+           0.34906461, 0.57650123, 0.54795542, 0.18056979, 0.00108256])
+
+
+
+
+![png](output_23_1.png)
+
+
+
+```python
+_ = [plt.plot((np.arange(len(p)) - len(p) // 2) / len(p) , *orient(p, c)) for p in binned_profiles[1:] for c, p in p.items() ]
+plt.xlabel('normalized major axis')
+plt.ylabel('normalized intensity')
+plt.legend(['TRITC', 'FITC'])
+plt.grid()
+```
+
+
+![png](output_27_0.png)
+